From b789f47546d5f59e2f30498758f074fad862bb01 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 12 Oct 2022 23:48:40 +0200 Subject: [PATCH 01/21] Add POC --- modules/nf-core/bowtie/align/main.nf | 1 + tests/config/nextflow.config | 1 + 2 files changed, 2 insertions(+) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index d2cba0e43cd..36c2ebb6f9e 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -5,6 +5,7 @@ process BOWTIE_ALIGN { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : + params.docker_url != null ? '${params.docker_url}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }" input: diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 2c672d49287..ce32a52136d 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -3,6 +3,7 @@ params { publish_dir_mode = "copy" enable_conda = false singularity_pull_docker_container = false + docker_url = "public.ecr.aws/biocontainers" } process { From b75a368460fc502b4a9778d70a78f16145cae8de Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 10:02:39 +0200 Subject: [PATCH 02/21] Try a defining a variable --- modules/nf-core/bowtie/align/main.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 36c2ebb6f9e..4a0c601953c 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,10 +3,12 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) + def docker_image = params.docker_url != null ? + '${params.docker_url}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : + 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : - params.docker_url != null ? '${params.docker_url}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : - 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }" + ${docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }" input: tuple val(meta), path(reads) From 91d2b9d97845bd405e51fd9f7ab27560f3a49a10 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 11:31:26 +0200 Subject: [PATCH 03/21] Add closure Co-authored-by: grst --- modules/nf-core/bowtie/align/main.nf | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 4a0c601953c..d7d2ea6e5b1 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,12 +3,9 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - def docker_image = params.docker_url != null ? - '${params.docker_url}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : - 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' : - ${docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }" + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" : + "${docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' } input: tuple val(meta), path(reads) From e04ebe1879c60fd84e5b41c414273923e6fbace9 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 11:32:05 +0200 Subject: [PATCH 04/21] fix: ' => " --- modules/nf-core/bowtie/align/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index d7d2ea6e5b1..14d67431955 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -5,7 +5,7 @@ process BOWTIE_ALIGN { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" : - "${docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' } + "${docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" } input: tuple val(meta), path(reads) From 0d5f1bb03877cf524eee191294816098c03ae8c7 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 11:32:44 +0200 Subject: [PATCH 05/21] fix: docker_url => params.docker_url --- modules/nf-core/bowtie/align/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 14d67431955..a0966cf5651 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -5,7 +5,7 @@ process BOWTIE_ALIGN { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" : - "${docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" } + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" } input: tuple val(meta), path(reads) From 6a2dfb07bfab61a6531e2a229857dc4ba7768f96 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 12:29:15 +0200 Subject: [PATCH 06/21] refactor: Add docker_url to all modules --- modules/nf-core/abacas/main.nf | 4 ++-- modules/nf-core/abricate/run/main.nf | 4 ++-- modules/nf-core/abricate/summary/main.nf | 4 ++-- modules/nf-core/adapterremoval/main.nf | 4 ++-- modules/nf-core/adapterremovalfixprefix/main.nf | 4 ++-- modules/nf-core/agrvate/main.nf | 4 ++-- modules/nf-core/allelecounter/main.nf | 4 ++-- modules/nf-core/ampir/main.nf | 4 ++-- modules/nf-core/amplify/predict/main.nf | 4 ++-- modules/nf-core/amps/main.nf | 4 ++-- modules/nf-core/amrfinderplus/run/main.nf | 4 ++-- modules/nf-core/amrfinderplus/update/main.nf | 4 ++-- modules/nf-core/angsd/docounts/main.nf | 4 ++-- modules/nf-core/antismash/antismashlite/main.nf | 4 ++-- .../antismash/antismashlitedownloaddatabases/main.nf | 4 ++-- modules/nf-core/aria2/main.nf | 4 ++-- modules/nf-core/ariba/getref/main.nf | 4 ++-- modules/nf-core/ariba/run/main.nf | 4 ++-- modules/nf-core/arriba/main.nf | 4 ++-- modules/nf-core/artic/guppyplex/main.nf | 4 ++-- modules/nf-core/artic/minion/main.nf | 4 ++-- modules/nf-core/ascat/main.nf | 4 ++-- modules/nf-core/assemblyscan/main.nf | 4 ++-- modules/nf-core/ataqv/ataqv/main.nf | 4 ++-- modules/nf-core/ataqv/mkarv/main.nf | 4 ++-- modules/nf-core/atlas/call/main.nf | 4 ++-- modules/nf-core/atlas/pmd/main.nf | 4 ++-- modules/nf-core/atlas/recal/main.nf | 4 ++-- modules/nf-core/atlas/splitmerge/main.nf | 4 ++-- modules/nf-core/bakta/main.nf | 4 ++-- modules/nf-core/bamaligncleaner/main.nf | 4 ++-- modules/nf-core/bamcmp/main.nf | 4 ++-- modules/nf-core/bamtools/convert/main.nf | 4 ++-- modules/nf-core/bamtools/split/main.nf | 4 ++-- modules/nf-core/bamtools/stats/main.nf | 4 ++-- modules/nf-core/bamutil/trimbam/main.nf | 4 ++-- modules/nf-core/bandage/image/main.nf | 4 ++-- modules/nf-core/bbmap/align/main.nf | 4 ++-- modules/nf-core/bbmap/bbduk/main.nf | 4 ++-- modules/nf-core/bbmap/bbsplit/main.nf | 4 ++-- modules/nf-core/bbmap/clumpify/main.nf | 4 ++-- modules/nf-core/bbmap/index/main.nf | 4 ++-- modules/nf-core/bbmap/pileup/main.nf | 4 ++-- modules/nf-core/bcftools/annotate/main.nf | 4 ++-- modules/nf-core/bcftools/concat/main.nf | 4 ++-- modules/nf-core/bcftools/consensus/main.nf | 4 ++-- modules/nf-core/bcftools/convert/main.nf | 4 ++-- modules/nf-core/bcftools/filter/main.nf | 4 ++-- modules/nf-core/bcftools/index/main.nf | 4 ++-- modules/nf-core/bcftools/isec/main.nf | 4 ++-- modules/nf-core/bcftools/merge/main.nf | 4 ++-- modules/nf-core/bcftools/mpileup/main.nf | 4 ++-- modules/nf-core/bcftools/norm/main.nf | 4 ++-- modules/nf-core/bcftools/query/main.nf | 4 ++-- modules/nf-core/bcftools/reheader/main.nf | 4 ++-- modules/nf-core/bcftools/roh/main.nf | 4 ++-- modules/nf-core/bcftools/sort/main.nf | 4 ++-- modules/nf-core/bcftools/stats/main.nf | 4 ++-- modules/nf-core/bcftools/view/main.nf | 4 ++-- modules/nf-core/bedtools/bamtobed/main.nf | 4 ++-- modules/nf-core/bedtools/complement/main.nf | 4 ++-- modules/nf-core/bedtools/genomecov/main.nf | 4 ++-- modules/nf-core/bedtools/getfasta/main.nf | 4 ++-- modules/nf-core/bedtools/intersect/main.nf | 4 ++-- modules/nf-core/bedtools/makewindows/main.nf | 4 ++-- modules/nf-core/bedtools/maskfasta/main.nf | 4 ++-- modules/nf-core/bedtools/merge/main.nf | 4 ++-- modules/nf-core/bedtools/slop/main.nf | 4 ++-- modules/nf-core/bedtools/sort/main.nf | 4 ++-- modules/nf-core/bedtools/split/main.nf | 4 ++-- modules/nf-core/bedtools/subtract/main.nf | 4 ++-- modules/nf-core/biobambam/bammarkduplicates2/main.nf | 2 +- modules/nf-core/biobambam/bammerge/main.nf | 4 ++-- modules/nf-core/biobambam/bamsormadup/main.nf | 2 +- modules/nf-core/biscuit/align/main.nf | 4 ++-- modules/nf-core/biscuit/biscuitblaster/main.nf | 4 ++-- modules/nf-core/biscuit/bsconv/main.nf | 4 ++-- modules/nf-core/biscuit/epiread/main.nf | 4 ++-- modules/nf-core/biscuit/index/main.nf | 4 ++-- modules/nf-core/biscuit/mergecg/main.nf | 4 ++-- modules/nf-core/biscuit/pileup/main.nf | 4 ++-- modules/nf-core/biscuit/qc/main.nf | 4 ++-- modules/nf-core/biscuit/vcf2bed/main.nf | 4 ++-- modules/nf-core/bismark/align/main.nf | 4 ++-- modules/nf-core/bismark/deduplicate/main.nf | 4 ++-- modules/nf-core/bismark/genomepreparation/main.nf | 4 ++-- modules/nf-core/bismark/methylationextractor/main.nf | 4 ++-- modules/nf-core/bismark/report/main.nf | 4 ++-- modules/nf-core/bismark/summary/main.nf | 4 ++-- modules/nf-core/blast/blastn/main.nf | 4 ++-- modules/nf-core/blast/makeblastdb/main.nf | 4 ++-- modules/nf-core/blast/tblastn/main.nf | 4 ++-- modules/nf-core/bowtie/build/main.nf | 4 ++-- modules/nf-core/bowtie2/align/main.nf | 4 ++-- modules/nf-core/bowtie2/build/main.nf | 4 ++-- modules/nf-core/bracken/bracken/main.nf | 4 ++-- modules/nf-core/bracken/combinebrackenoutputs/main.nf | 4 ++-- modules/nf-core/busco/main.nf | 4 ++-- modules/nf-core/bwa/aln/main.nf | 4 ++-- modules/nf-core/bwa/index/main.nf | 4 ++-- modules/nf-core/bwa/mem/main.nf | 4 ++-- modules/nf-core/bwa/sampe/main.nf | 4 ++-- modules/nf-core/bwa/samse/main.nf | 4 ++-- modules/nf-core/bwamem2/index/main.nf | 4 ++-- modules/nf-core/bwamem2/mem/main.nf | 4 ++-- modules/nf-core/bwameth/align/main.nf | 4 ++-- modules/nf-core/bwameth/index/main.nf | 4 ++-- modules/nf-core/cat/cat/main.nf | 4 ++-- modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/centrifuge/centrifuge/main.nf | 4 ++-- modules/nf-core/centrifuge/kreport/main.nf | 4 ++-- modules/nf-core/checkm/lineagewf/main.nf | 4 ++-- modules/nf-core/checkm/qa/main.nf | 4 ++-- modules/nf-core/chromap/chromap/main.nf | 4 ++-- modules/nf-core/chromap/index/main.nf | 4 ++-- modules/nf-core/clonalframeml/main.nf | 4 ++-- modules/nf-core/cmseq/polymut/main.nf | 4 ++-- modules/nf-core/cnvkit/antitarget/main.nf | 4 ++-- modules/nf-core/cnvkit/batch/main.nf | 4 ++-- modules/nf-core/cnvkit/reference/main.nf | 4 ++-- modules/nf-core/cnvpytor/callcnvs/main.nf | 4 ++-- modules/nf-core/cnvpytor/histogram/main.nf | 4 ++-- modules/nf-core/cnvpytor/importreaddepth/main.nf | 4 ++-- modules/nf-core/cnvpytor/partition/main.nf | 4 ++-- modules/nf-core/cnvpytor/view/main.nf | 4 ++-- modules/nf-core/controlfreec/assesssignificance/main.nf | 4 ++-- modules/nf-core/controlfreec/freec/main.nf | 4 ++-- modules/nf-core/controlfreec/freec2bed/main.nf | 4 ++-- modules/nf-core/controlfreec/freec2circos/main.nf | 4 ++-- modules/nf-core/controlfreec/makegraph/main.nf | 4 ++-- modules/nf-core/cooler/cload/main.nf | 4 ++-- modules/nf-core/cooler/digest/main.nf | 4 ++-- modules/nf-core/cooler/dump/main.nf | 4 ++-- modules/nf-core/cooler/merge/main.nf | 4 ++-- modules/nf-core/cooler/zoomify/main.nf | 4 ++-- modules/nf-core/crumble/main.nf | 4 ++-- modules/nf-core/csvtk/concat/main.nf | 4 ++-- modules/nf-core/csvtk/split/main.nf | 4 ++-- modules/nf-core/custom/dumpsoftwareversions/main.nf | 4 ++-- modules/nf-core/custom/getchromsizes/main.nf | 4 ++-- modules/nf-core/custom/sratoolsncbisettings/main.nf | 4 ++-- modules/nf-core/cutadapt/main.nf | 4 ++-- modules/nf-core/damageprofiler/main.nf | 4 ++-- modules/nf-core/dastool/dastool/main.nf | 4 ++-- modules/nf-core/dastool/fastatocontig2bin/main.nf | 4 ++-- modules/nf-core/dastool/scaffolds2bin/main.nf | 4 ++-- modules/nf-core/dedup/main.nf | 4 ++-- modules/nf-core/deeparg/downloaddata/main.nf | 6 +++--- modules/nf-core/deeparg/predict/main.nf | 6 +++--- modules/nf-core/deepbgc/download/main.nf | 4 ++-- modules/nf-core/deepbgc/pipeline/main.nf | 4 ++-- modules/nf-core/deeptools/bamcoverage/main.nf | 4 ++-- modules/nf-core/deeptools/computematrix/main.nf | 4 ++-- modules/nf-core/deeptools/plotfingerprint/main.nf | 4 ++-- modules/nf-core/deeptools/plotheatmap/main.nf | 4 ++-- modules/nf-core/deeptools/plotprofile/main.nf | 4 ++-- modules/nf-core/delly/call/main.nf | 4 ++-- modules/nf-core/diamond/blastp/main.nf | 4 ++-- modules/nf-core/diamond/blastx/main.nf | 4 ++-- modules/nf-core/diamond/makedb/main.nf | 4 ++-- modules/nf-core/dragmap/align/main.nf | 4 ++-- modules/nf-core/dragmap/hashtable/main.nf | 4 ++-- modules/nf-core/dragonflye/main.nf | 4 ++-- modules/nf-core/dshbio/exportsegments/main.nf | 4 ++-- modules/nf-core/dshbio/filterbed/main.nf | 4 ++-- modules/nf-core/dshbio/filtergff3/main.nf | 4 ++-- modules/nf-core/dshbio/splitbed/main.nf | 4 ++-- modules/nf-core/dshbio/splitgff3/main.nf | 4 ++-- modules/nf-core/ectyper/main.nf | 4 ++-- modules/nf-core/eido/convert/main.nf | 2 +- modules/nf-core/eido/validate/main.nf | 2 +- modules/nf-core/elprep/filter/main.nf | 4 ++-- modules/nf-core/elprep/merge/main.nf | 4 ++-- modules/nf-core/elprep/split/main.nf | 4 ++-- modules/nf-core/emboss/seqret/main.nf | 4 ++-- modules/nf-core/emmtyper/main.nf | 4 ++-- modules/nf-core/endorspy/main.nf | 4 ++-- modules/nf-core/ensemblvep/main.nf | 4 ++-- modules/nf-core/entrezdirect/esearch/main.nf | 4 ++-- modules/nf-core/entrezdirect/esummary/main.nf | 4 ++-- modules/nf-core/entrezdirect/xtract/main.nf | 4 ++-- modules/nf-core/epang/main.nf | 4 ++-- modules/nf-core/expansionhunter/main.nf | 4 ++-- modules/nf-core/faqcs/main.nf | 4 ++-- modules/nf-core/fargene/main.nf | 4 ++-- modules/nf-core/fastani/main.nf | 4 ++-- modules/nf-core/fastawindows/main.nf | 4 ++-- modules/nf-core/fastp/main.nf | 4 ++-- modules/nf-core/fastqc/main.nf | 4 ++-- modules/nf-core/fastqscan/main.nf | 4 ++-- modules/nf-core/fasttree/main.nf | 4 ++-- modules/nf-core/fcs/fcsadaptor/main.nf | 2 +- modules/nf-core/ffq/main.nf | 4 ++-- modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 4 ++-- modules/nf-core/fgbio/fastqtobam/main.nf | 4 ++-- modules/nf-core/fgbio/groupreadsbyumi/main.nf | 4 ++-- modules/nf-core/fgbio/sortbam/main.nf | 4 ++-- modules/nf-core/fgbio/zipperbams/main.nf | 4 ++-- modules/nf-core/filtlong/main.nf | 4 ++-- modules/nf-core/flash/main.nf | 4 ++-- modules/nf-core/flye/main.nf | 4 ++-- modules/nf-core/fq/lint/main.nf | 4 ++-- modules/nf-core/freebayes/main.nf | 4 ++-- modules/nf-core/gamma/gamma/main.nf | 4 ++-- modules/nf-core/gappa/examineassign/main.nf | 4 ++-- modules/nf-core/gappa/examinegraft/main.nf | 4 ++-- modules/nf-core/gappa/examineheattree/main.nf | 4 ++-- modules/nf-core/gatk/indelrealigner/main.nf | 4 ++-- modules/nf-core/gatk/realignertargetcreator/main.nf | 4 ++-- modules/nf-core/gatk/unifiedgenotyper/main.nf | 4 ++-- modules/nf-core/gatk4/applybqsr/main.nf | 4 ++-- modules/nf-core/gatk4/applyvqsr/main.nf | 4 ++-- modules/nf-core/gatk4/baserecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/bedtointervallist/main.nf | 4 ++-- modules/nf-core/gatk4/calculatecontamination/main.nf | 4 ++-- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 4 ++-- modules/nf-core/gatk4/collectreadcounts/main.nf | 4 ++-- modules/nf-core/gatk4/collectsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/combinegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/composestrtablefile/main.nf | 4 ++-- modules/nf-core/gatk4/createsequencedictionary/main.nf | 4 ++-- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 4 ++-- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 4 ++-- modules/nf-core/gatk4/fastqtosam/main.nf | 4 ++-- modules/nf-core/gatk4/filtermutectcalls/main.nf | 4 ++-- modules/nf-core/gatk4/filtervarianttranches/main.nf | 4 ++-- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 4 ++-- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- modules/nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/getpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/haplotypecaller/main.nf | 4 ++-- modules/nf-core/gatk4/indexfeaturefile/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttobed/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttools/main.nf | 4 ++-- modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 4 ++-- modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 4 ++-- modules/nf-core/gatk4/markduplicates/main.nf | 4 ++-- modules/nf-core/gatk4/mergebamalignment/main.nf | 4 ++-- modules/nf-core/gatk4/mergemutectstats/main.nf | 4 ++-- modules/nf-core/gatk4/mergevcfs/main.nf | 4 ++-- modules/nf-core/gatk4/mutect2/main.nf | 4 ++-- modules/nf-core/gatk4/printsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/reblockgvcf/main.nf | 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modules/nf-core/subread/featurecounts/main.nf | 4 ++-- modules/nf-core/svdb/merge/main.nf | 4 ++-- modules/nf-core/svdb/query/main.nf | 4 ++-- modules/nf-core/svtk/standardize/main.nf | 4 ++-- modules/nf-core/tabix/bgzip/main.nf | 4 ++-- modules/nf-core/tabix/bgziptabix/main.nf | 4 ++-- modules/nf-core/tabix/tabix/main.nf | 4 ++-- modules/nf-core/tailfindr/main.nf | 4 ++-- modules/nf-core/tbprofiler/profile/main.nf | 4 ++-- modules/nf-core/tiddit/cov/main.nf | 4 ++-- modules/nf-core/tiddit/sv/main.nf | 4 ++-- modules/nf-core/transdecoder/longorf/main.nf | 2 +- modules/nf-core/transdecoder/predict/main.nf | 2 +- modules/nf-core/trimgalore/main.nf | 4 ++-- modules/nf-core/trimmomatic/main.nf | 4 ++-- modules/nf-core/ucsc/bedclip/main.nf | 4 ++-- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 4 ++-- modules/nf-core/ucsc/bedtobigbed/main.nf | 4 ++-- modules/nf-core/ucsc/bigwigaverageoverbed/main.nf | 4 ++-- modules/nf-core/ucsc/liftover/main.nf | 4 ++-- modules/nf-core/ucsc/wigtobigwig/main.nf | 4 ++-- modules/nf-core/ultra/align/main.nf | 4 ++-- modules/nf-core/ultra/index/main.nf | 4 ++-- modules/nf-core/ultra/pipeline/main.nf | 4 ++-- modules/nf-core/umitools/dedup/main.nf | 4 ++-- modules/nf-core/umitools/extract/main.nf | 4 ++-- modules/nf-core/unicycler/main.nf | 4 ++-- modules/nf-core/untar/main.nf | 2 +- modules/nf-core/unzip/main.nf | 4 ++-- modules/nf-core/vardictjava/main.nf | 4 ++-- modules/nf-core/variantbam/main.nf | 4 ++-- modules/nf-core/vcf2db/main.nf | 4 ++-- modules/nf-core/vcf2maf/main.nf | 4 ++-- modules/nf-core/vcfanno/main.nf | 4 ++-- modules/nf-core/vcflib/vcfbreakmulti/main.nf | 4 ++-- modules/nf-core/vcflib/vcfuniq/main.nf | 4 ++-- modules/nf-core/vcftools/main.nf | 4 ++-- modules/nf-core/verifybamid/verifybamid2/main.nf | 4 ++-- modules/nf-core/vsearch/sintax/main.nf | 4 ++-- modules/nf-core/vsearch/usearchglobal/main.nf | 4 ++-- modules/nf-core/wgsim/main.nf | 4 ++-- modules/nf-core/whamg/main.nf | 4 ++-- modules/nf-core/yara/index/main.nf | 4 ++-- modules/nf-core/yara/mapper/main.nf | 4 ++-- tests/modules/nf-core/vcf2maf/nextflow.config | 2 +- 620 files changed, 1227 insertions(+), 1227 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index 00c9169f5c7..389e8bc649a 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -3,9 +3,9 @@ process ABACAS { label 'process_medium' conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : - 'quay.io/biocontainers/abacas:1.3.1--pl526_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/abacas:1.3.1--pl526_0" } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index 11992791551..c6a82be2dbc 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -3,9 +3,9 @@ process ABRICATE_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': - 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index 620fd42a01e..13281db950b 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -3,9 +3,9 @@ process ABRICATE_SUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': - 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 0e17c055cde..1a779751ca5 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -3,9 +3,9 @@ process ADAPTERREMOVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : - 'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/adapterremoval:2.3.2--hb7ba0dd_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 449146c86e0..595697c43df 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -4,9 +4,9 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2': - 'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/adapterremovalfixprefix:0.0.5--hdfd78af_2" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 8503505d145..c519b2a6f21 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -3,9 +3,9 @@ process AGRVATE { label 'process_low' conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' : - 'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/agrvate:1.0.2--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index b2cb1b0c0eb..3127d5608d9 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -3,9 +3,9 @@ process ALLELECOUNTER { label 'process_low' conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' : - 'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cancerit-allelecount:4.3.0--h41abebc_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index ae4c5b69c9a..e4f2c0213cf 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -3,9 +3,9 @@ process AMPIR { label 'process_single' conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0': - 'quay.io/biocontainers/r-ampir:1.1.0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/r-ampir:1.1.0" } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 41c0f7aa348..9eace6d397b 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -4,9 +4,9 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0': - 'quay.io/biocontainers/amplify:1.0.3--py36hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/amplify:1.0.3--py36hdfd78af_0" } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 57cdcff8f12..2f6592712e7 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -2,9 +2,9 @@ process AMPS { label 'process_low' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : - 'quay.io/biocontainers/hops:0.35--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 3b15bee77d8..080b2b501b6 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -3,9 +3,9 @@ process AMRFINDERPLUS_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': - 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index e4e6300618e..50ab02dbfdb 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -3,9 +3,9 @@ process AMRFINDERPLUS_UPDATE { label 'process_single' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': - 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index 41c4075a1b3..bbeeb24de3d 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -3,9 +3,9 @@ process ANGSD_DOCOUNTS { label 'process_low' conda (params.enable_conda ? "bioconda::angsd=0.939" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0': - 'quay.io/biocontainers/angsd:0.939--h468462d_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/angsd:0.939--h468462d_0" } input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 921b6e254b3..7bbfcfef4fb 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -3,9 +3,9 @@ process ANTISMASH_ANTISMASHLITE { label 'process_medium' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : - 'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } containerOptions { workflow.containerEngine == 'singularity' ? diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 0100acc7741..904243d3f27 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,9 +2,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { label 'process_single' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : - 'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 27437467a38..4c55b561cd7 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -4,9 +4,9 @@ process ARIA2 { label 'process_single' conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/aria2:1.36.0' : - 'quay.io/biocontainers/aria2:1.36.0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/aria2:1.36.0" } input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index 452803cfb51..5f3f94d6dc4 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -3,9 +3,9 @@ process ARIBA_GETREF { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': - 'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 75b2ea15825..044cc8a93f2 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -3,9 +3,9 @@ process ARIBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': - 'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 8c4dfcb25ef..c870717c174 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -3,9 +3,9 @@ process ARRIBA { label 'process_medium' conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : - 'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/arriba:2.3.0--haa8aa89_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 2fd518e03ae..81e3a081a54 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -3,9 +3,9 @@ process ARTIC_GUPPYPLEX { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : - 'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index 1629d433800..39212c7061f 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -3,9 +3,9 @@ process ARTIC_MINION { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : - 'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index df6141d0107..b5238880152 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -3,9 +3,9 @@ process ASCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': - 'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" } input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 889f92a9c5e..3fa07f860d7 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -3,9 +3,9 @@ process ASSEMBLYSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' : - 'quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/assembly-scan:0.4.1--pyhdfd78af_0" } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index c8a6c3ac60c..61d44602d1b 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -3,9 +3,9 @@ process ATAQV_ATAQV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' : - 'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } input: tuple val(meta), path(bam), path(bai), path(peak_file) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 3a0550d4a26..310461ddd87 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -2,9 +2,9 @@ process ATAQV_MKARV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2': - 'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 30b34d34a2a..e33ddb5c22e 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -3,9 +3,9 @@ process ATLAS_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - 'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index 38abc0dbc50..3c3197b07ed 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -3,9 +3,9 @@ process ATLAS_PMD { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - 'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index fa3764e89d9..10368c9812e 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -3,9 +3,9 @@ process ATLAS_RECAL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - 'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index b7b07bfb3c5..b47e3cf6aa1 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -3,9 +3,9 @@ process ATLAS_SPLITMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - 'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index 0b4b7b692ad..6c28af0bddf 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -3,9 +3,9 @@ process BAKTA { label 'process_medium' conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bakta:1.5.0--pyhdfd78af_0' : - 'quay.io/biocontainers/bakta:1.5.0--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bakta:1.5.0--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index 922b72e6845..70f9903afeb 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -3,9 +3,9 @@ process BAMALIGNCLEANER { label 'process_low' conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' : - 'quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bamaligncleaner:0.2.1--pyhdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 534f0d41107..49963eafe5f 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -3,9 +3,9 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' : - 'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bamcmp:2.2--h05f6578_0" } input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index efe2849746e..d10136a4ebc 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -3,9 +3,9 @@ process BAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : - 'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index aaa5b663372..70843cac54f 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -3,9 +3,9 @@ process BAMTOOLS_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' : - 'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bamtools:2.5.2--hd03093a_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index db46ce11b5f..edeb1a1514f 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -3,9 +3,9 @@ process BAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : - 'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 07203070f04..e02207abab4 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -3,9 +3,9 @@ process BAMUTIL_TRIMBAM { label 'process_single' conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' : - 'quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bamutil:1.0.15--h2e03b76_1" } input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index ee504a129d9..7a5f1789aeb 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -3,9 +3,9 @@ process BANDAGE_IMAGE { label 'process_low' conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' : - 'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bandage:0.8.1--hc9558a2_2" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index aa1fbe1a31c..07b20f31530 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -3,9 +3,9 @@ process BBMAP_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : - 'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 0ae005e4065..4ebe50f58d1 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -3,9 +3,9 @@ process BBMAP_BBDUK { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : - 'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.90--he522d1c_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index b55929ce92b..ab8dda8dff3 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,9 +2,9 @@ process BBMAP_BBSPLIT { label 'process_high' conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' : - 'quay.io/biocontainers/bbmap:38.93--he522d1c_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.93--he522d1c_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index 107e91702ec..e8758bf4df6 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -4,9 +4,9 @@ process BBMAP_CLUMPIFY { label 'process_high_memory' conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.98--h5c4e2a8_1' : - 'quay.io/biocontainers/bbmap:38.98--h5c4e2a8_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.98--h5c4e2a8_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index fdd6d102008..c461b0b9eb4 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -3,9 +3,9 @@ process BBMAP_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' : - 'quay.io/biocontainers/bbmap:38.92--he522d1c_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.92--he522d1c_0" } input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 1f34efc5640..7c31fbb6509 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -3,9 +3,9 @@ process BBMAP_PILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : - 'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index da94d3c0500..8e46974eacc 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_ANNOTATE { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index d2a58a557a7..162d1e4a85e 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_CONCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index e28dc7f4b04..d957a493945 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index f184c2f91a4..5f7c1234d99 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_CONVERT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index ef99eda2e3e..63d05ef631b 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 119019fc239..f49379e274c 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 43d7b136307..1801c21e5df 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_ISEC { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index af586cd12d2..124c41cf98c 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index b7795bfc4ff..cb07045c254 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_MPILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 96f306bc8b1..0fba8b9ed7e 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_NORM { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 5de34a9ebd6..82f66c31fa7 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 457cf4d9cd3..c36fdb420c4 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_REHEADER { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 83ac4e65b88..323f27579e3 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_ROH { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 9552b57c49d..cd39c32d12e 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 6a755c0e21e..3d9eb0a6dd6 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 3df08a57426..5a8eabda681 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -3,9 +3,9 @@ process BCFTOOLS_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index e3d3ee21fa5..2d3a1ce155a 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_BAMTOBED { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index d539dbdb63a..d7b6e457830 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_COMPLEMENT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 05e359c955b..a40ef1534fd 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 80d828ad5fa..3f753cd5392 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_GETFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: path bed diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index 2dee297c328..de1e05d3087 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_INTERSECT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index b15c38ff10f..c097d3aa68b 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_MAKEWINDOWS { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' : - 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_1" } input: tuple val(meta), path(regions) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index 3e17a0a7c9a..acf928eb90d 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_MASKFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index ba7cd9eb5a3..615e3257766 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index e68a5860db6..a510b9e0cff 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_SLOP { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 17b224d5e27..dc61624e237 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_SORT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index aaa5497d3ea..cfefcb88f66 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_SPLIT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h468198e_3': - 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_2" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index f99673c41e0..f39bcdda0f7 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -3,9 +3,9 @@ process BEDTOOLS_SUBTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/modules/nf-core/biobambam/bammarkduplicates2/main.nf index dd0e55b692d..33c84aa4738 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -3,7 +3,7 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 { label 'process_medium' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}" + container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_url ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index 75040903a46..6d92a5af004 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -3,9 +3,9 @@ process BIOBAMBAM_BAMMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1': - 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index 18406ede51d..95066cead19 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -3,7 +3,7 @@ process BIOBAMBAM_BAMSORMADUP { label "process_medium" conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}" + container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_url ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} input: tuple val(meta), path(bams, stageAs: "?/*") diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index 18e178ffbac..cac25d9aaee 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -3,9 +3,9 @@ process BISCUIT_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - 'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 700bc5e04b8..2605bf788b0 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -3,9 +3,9 @@ process BISCUIT_BLASTER { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - 'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index 8c5ee91f627..aac47a75d48 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -3,9 +3,9 @@ process BISCUIT_BSCONV { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - 'quay.io/biocontainers/biscuit:1.0.2.20220113--h81a5ba2_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index bc8c6d9f94e..1f9ac0fbd38 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -3,9 +3,9 @@ process BISCUIT_EPIREAD { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - 'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(bam), path(bai), path(snp_bed) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 9aa04330bd0..24755a26992 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -3,9 +3,9 @@ process BISCUIT_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - 'quay.io/biocontainers/biscuit:1.0.2.20220113--h81a5ba2_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index 6cafdb36c0c..3e38f00d444 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -3,9 +3,9 @@ process BISCUIT_MERGECG { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - 'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index dcddc41841d..69daab9aad3 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -3,9 +3,9 @@ process BISCUIT_PILEUP { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - 'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index dea6473b749..38771a969a0 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -3,9 +3,9 @@ process BISCUIT_QC { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - 'quay.io/biocontainers/biscuit:1.0.2.20220113--h81a5ba2_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 7bbcc826fd6..30771e6466e 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -3,9 +3,9 @@ process BISCUIT_VCF2BED { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - 'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index eeddcabb2ba..dcb71b0c7fe 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -3,9 +3,9 @@ process BISMARK_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - 'quay.io/biocontainers/bismark:0.23.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index ea763774aaf..19bd159436d 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -3,9 +3,9 @@ process BISMARK_DEDUPLICATE { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - 'quay.io/biocontainers/bismark:0.23.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 59c495c5196..de1136c68ac 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -3,9 +3,9 @@ process BISMARK_GENOMEPREPARATION { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - 'quay.io/biocontainers/bismark:0.23.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 5543ab7e8cb..8a9e42cf3e8 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -3,9 +3,9 @@ process BISMARK_METHYLATIONEXTRACTOR { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - 'quay.io/biocontainers/bismark:0.23.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index bec3de99ea3..1498b638423 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -3,9 +3,9 @@ process BISMARK_REPORT { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - 'quay.io/biocontainers/bismark:0.23.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 49fec53e24f..ce2828cddae 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -2,9 +2,9 @@ process BISMARK_SUMMARY { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - 'quay.io/biocontainers/bismark:0.23.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: path(bam) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index b85f6c8ecb7..78ca59afc1c 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -3,9 +3,9 @@ process BLAST_BLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 12208ea89c6..6aabd511c5b 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -3,9 +3,9 @@ process BLAST_MAKEBLASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 7eafb321958..7189502c520 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -3,9 +3,9 @@ process BLAST_TBLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index e01d9855d16..0e9abae6cd2 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -3,9 +3,9 @@ process BOWTIE_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : - 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bowtie:1.3.0--py38hed8969a_1" } input: path fasta diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index c74e376f7f0..0bbd3b0ea45 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -3,9 +3,9 @@ process BOWTIE2_ALIGN { label "process_high" conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) - container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" : - "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index a4da62d073b..67c20960439 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -3,9 +3,9 @@ process BOWTIE2_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : - 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bowtie2:2.4.4--py39hbb4e92a_0" } input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index 5e08418966d..ac082102b2e 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -5,9 +5,9 @@ process BRACKEN_BRACKEN { // WARN: Version information not provided by tool on CLI. // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': - 'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } input: tuple val(meta), path(kraken_report) diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 73b7148ac3d..439505a948f 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,9 +2,9 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { label 'process_low' conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': - 'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 483768f14e1..cc94cf75ff5 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -3,9 +3,9 @@ process BUSCO { label 'process_medium' conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0': - 'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/busco:5.4.3--pyhdfd78af_0" } input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 741c01596ae..8e587b678a2 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -3,9 +3,9 @@ process BWA_ALN { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8' : - 'quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bwa:0.7.17--h5bf99c6_8" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index aa75ae5dbb0..1710d6e0340 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -3,9 +3,9 @@ process BWA_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : - 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bwa:0.7.17--hed695b0_7" } input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index f55af944377..1c72dd77788 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -3,9 +3,9 @@ process BWA_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index cfe9529ddf9..4c460bbf71b 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -3,9 +3,9 @@ process BWA_SAMPE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index fed412f2e15..a2112db87f0 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -3,9 +3,9 @@ process BWA_SAMSE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 0b7ad1991e3..2be4347353f 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -3,9 +3,9 @@ process BWAMEM2_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : - 'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bwa-mem2:2.2.1--he513fc3_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 08dc5dfb8cf..787e6db9bf6 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -3,9 +3,9 @@ process BWAMEM2_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : - 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 6d9c4431826..925dbc2ada1 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -3,9 +3,9 @@ process BWAMETH_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - 'quay.io/biocontainers/bwameth:0.2.2--py_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 4c1068268ae..2e2f4aff083 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -3,9 +3,9 @@ process BWAMETH_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - 'quay.io/biocontainers/bwameth:0.2.2--py_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 40e53f3edaa..3da462e33db 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -3,9 +3,9 @@ process CAT_CAT { label 'process_low' conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : - 'quay.io/biocontainers/pigz:2.3.4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pigz:2.3.4" } input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 4fa365d33e6..d761b319f67 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,7 +3,7 @@ process CAT_FASTQ { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 3d23fc961fb..59b3968e949 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -3,9 +3,9 @@ process CENTRIFUGE_CENTRIFUGE { label 'process_high' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : - 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 8e5b741a1f2..512b7c7583d 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -3,9 +3,9 @@ process CENTRIFUGE_KREPORT { label 'process_single' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': - 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index db0535e1007..0e82563b763 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -3,9 +3,9 @@ process CHECKM_LINEAGEWF { label 'process_medium' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - 'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 80b9747f152..9716dfe4126 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -3,9 +3,9 @@ process CHECKM_QA { label 'process_low' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - 'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index 137f0340c71..437624f2dc9 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -3,9 +3,9 @@ process CHROMAP_CHROMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' : - 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index ee3706959ea..545e1052911 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -3,9 +3,9 @@ process CHROMAP_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : - 'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/chromap:0.2.1--hd03093a_0" } input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 24502796b9e..9b7d74fd3b6 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -3,9 +3,9 @@ process CLONALFRAMEML { label 'process_low' conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/clonalframeml:1.12--h7d875b9_1' : - 'quay.io/biocontainers/clonalframeml:1.12--h7d875b9_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/clonalframeml:1.12--h7d875b9_1" } input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index 8a774e230d1..6cdeabf1a93 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -4,9 +4,9 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' : - 'quay.io/biocontainers/cmseq:1.0.4--pyhb7b1952_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cmseq:1.0.4--pyhb7b1952_0" } input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index bf6461bdb08..fc7062a6675 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -3,9 +3,9 @@ process CNVKIT_ANTITARGET { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 090f7860d2e..f59f255b8d2 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -3,9 +3,9 @@ process CNVKIT_BATCH { label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' : - 'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" } input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 10458f2786b..d98f4b9a7f5 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -3,9 +3,9 @@ process CNVKIT_REFERENCE { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } input: path fasta diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index 021cd879629..69c1a41568e 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -3,9 +3,9 @@ process CNVPYTOR_CALLCNVS { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 2abb96e62df..77788a5db45 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -3,9 +3,9 @@ process CNVPYTOR_HISTOGRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index fd09d1c778f..52419e8e9e8 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -3,9 +3,9 @@ process CNVPYTOR_IMPORTREADDEPTH { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(input_file), path(index) diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index d32741ba382..89ac65f9dd9 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -3,9 +3,9 @@ process CNVPYTOR_PARTITION { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index 153f43e8c91..ad4a1ddee79 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -3,9 +3,9 @@ process CNVPYTOR_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor_files) diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 4bdb00b386b..d7050c9e2e7 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -3,9 +3,9 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 857ffdee171..630d50153ac 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -3,9 +3,9 @@ process CONTROLFREEC_FREEC { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index aefc200e811..a9ea2aca7fd 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -3,9 +3,9 @@ process CONTROLFREEC_FREEC2BED { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 8f9be30097c..aa2b12f1477 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -3,9 +3,9 @@ process CONTROLFREEC_FREEC2CIRCOS { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index a8954d726ab..cf8ca736d70 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -3,9 +3,9 @@ process CONTROLFREEC_MAKEGRAPH { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 52964b8dd93..2d9bd85e9e4 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -3,9 +3,9 @@ process COOLER_CLOAD { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(pairs), path(index) diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index 7e8e36f0b02..83f4e35ead9 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -3,9 +3,9 @@ process COOLER_DIGEST { label 'process_medium' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: path fasta diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index 996e9b5bfbc..4ef275496b7 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -3,9 +3,9 @@ process COOLER_DUMP { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index 1e439cafbb8..d442d8a8ae0 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -3,9 +3,9 @@ process COOLER_MERGE { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 942282c0d6a..6af32477b9e 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -3,9 +3,9 @@ process COOLER_ZOOMIFY { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index caf33b26d60..14a1a3a31dd 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -3,9 +3,9 @@ process CRUMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/crumble:0.9.0--hb0d9459_1': - 'quay.io/biocontainers/crumble:0.9.0--hb0d9459_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/crumble:0.9.0--hb0d9459_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index f30e8332a0e..8d72d097356 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -3,9 +3,9 @@ process CSVTK_CONCAT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - 'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 5653d192a3f..f3a1ae7e8d1 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -3,9 +3,9 @@ process CSVTK_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - 'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cebb6e0589a..d87ad0c6512 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -3,9 +3,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 8e1693d40b6..2191a3d6473 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -3,9 +3,9 @@ process CUSTOM_GETCHROMSIZES { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 21bf3005285..7428131097e 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -3,9 +3,9 @@ process CUSTOM_SRATOOLSNCBISETTINGS { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : - 'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } output: path('*.mkfg') , emit: ncbi_settings diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 9b310c0e693..95c568cec7c 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -3,9 +3,9 @@ process CUTADAPT { label 'process_medium' conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : - 'quay.io/biocontainers/cutadapt:3.4--py39h38f01e4_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/cutadapt:3.4--py39h38f01e4_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index 7b2392a71dd..3c26f190c8b 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -3,9 +3,9 @@ process DAMAGEPROFILER { label 'process_single' conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' : - 'quay.io/biocontainers/damageprofiler:1.1--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/damageprofiler:1.1--hdfd78af_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index a7d9c6f6e18..6c7faa55b27 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -3,9 +3,9 @@ process DASTOOL_DASTOOL { label 'process_medium' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : - 'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index d9e88be778e..3ee3f8b5103 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -3,9 +3,9 @@ process DASTOOL_FASTATOCONTIG2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : - 'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 36c287208d8..6c9b7ed4cd4 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -3,9 +3,9 @@ process DASTOOL_SCAFFOLDS2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : - 'quay.io/biocontainers/das_tool:1.1.3--r41hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/das_tool:1.1.3--r41hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index 7dbbd6da282..53d73a0d710 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -3,9 +3,9 @@ process DEDUP { label 'process_single' conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1' : - 'quay.io/biocontainers/dedup:0.12.8--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dedup:0.12.8--hdfd78af_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index c06e623cbeb..d2c5617701d 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,14 +2,14 @@ process DEEPARG_DOWNLOADDATA { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - 'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ - containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } + containerOptions { {workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } input: diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 7aef879fc58..f7378a6abbf 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -3,14 +3,14 @@ process DEEPARG_PREDICT { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - 'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ - containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } + containerOptions { {workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } input: tuple val(meta), path(fasta), val(model) diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 702e3c989f5..d978c8677ed 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -2,9 +2,9 @@ process DEEPBGC_DOWNLOAD { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - 'quay.io/biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index 6d8ef5f1ef1..4c488342694 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -3,9 +3,9 @@ process DEEPBGC_PIPELINE { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - 'quay.io/biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 04073ed9482..5275cedf79f 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -3,9 +3,9 @@ process DEEPTOOLS_BAMCOVERAGE { label 'process_low' conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0': - 'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 96dfef3c602..8e91d05d965 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -3,9 +3,9 @@ process DEEPTOOLS_COMPUTEMATRIX { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - 'quay.io/biocontainers/deeptools:3.5.1--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index 83613be7b3d..3b75edd85c5 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -3,9 +3,9 @@ process DEEPTOOLS_PLOTFINGERPRINT { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - 'quay.io/biocontainers/deeptools:3.5.1--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index 1e402e3919c..3c730dd3a02 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -3,9 +3,9 @@ process DEEPTOOLS_PLOTHEATMAP { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - 'quay.io/biocontainers/deeptools:3.5.1--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index d83a9493876..27ed76e37d8 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -3,9 +3,9 @@ process DEEPTOOLS_PLOTPROFILE { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - 'quay.io/biocontainers/deeptools:3.5.1--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index 57bb537a21c..e329f5c4a7f 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -3,9 +3,9 @@ process DELLY_CALL { label 'process_medium' conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/delly:1.1.5--h358d541_0' : - 'quay.io/biocontainers/delly:1.1.5--h358d541_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/delly:1.1.5--h358d541_0" } input: tuple val(meta), path(input), path(input_index), path(exclude_bed) diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index 033186eaf03..0651a7833c9 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -3,9 +3,9 @@ process DIAMOND_BLASTP { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 1f4ff257c2b..f28abd2ee88 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -3,9 +3,9 @@ process DIAMOND_BLASTX { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index a76a94e5c95..cc8e1eb5fd0 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -3,9 +3,9 @@ process DIAMOND_MAKEDB { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index f0d59f05f67..7562f64212f 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -3,9 +3,9 @@ process DRAGMAP_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': - 'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 81333dfdae1..54e3c531e16 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -3,9 +3,9 @@ process DRAGMAP_HASHTABLE { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0': - 'quay.io/biocontainers/dragmap:1.2.1--hd4ca14e_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dragmap:1.2.1--hd4ca14e_0" } input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index 91b009d45c4..16383de2e68 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -3,9 +3,9 @@ process DRAGONFLYE { label 'process_medium' conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' : - 'quay.io/biocontainers/dragonflye:1.0.11--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dragonflye:1.0.11--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index d2e83a9e756..095a88600cd 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -3,9 +3,9 @@ process DSHBIO_EXPORTSEGMENTS { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - 'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 74dba7c4ec0..7299b4081e9 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -3,9 +3,9 @@ process DSHBIO_FILTERBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - 'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index 155ec399b76..cba9ed7dfb0 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -3,9 +3,9 @@ process DSHBIO_FILTERGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - 'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index 409df2e8247..7c256dfaff8 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -3,9 +3,9 @@ process DSHBIO_SPLITBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - 'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 4e92306944d..95362f5abb9 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -3,9 +3,9 @@ process DSHBIO_SPLITGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - 'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 34973ee6c9b..65bf40fa64d 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -3,9 +3,9 @@ process ECTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1' : - 'quay.io/biocontainers/ectyper:1.0.0--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ectyper:1.0.0--pyhdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/eido/convert/main.nf b/modules/nf-core/eido/convert/main.nf index 7ec4b8cdd0f..8450fb34025 100644 --- a/modules/nf-core/eido/convert/main.nf +++ b/modules/nf-core/eido/convert/main.nf @@ -3,7 +3,7 @@ process EIDO_CONVERT { label 'process_single' conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' : 'biocontainers/eido:0.1.9_cv1' }" diff --git a/modules/nf-core/eido/validate/main.nf b/modules/nf-core/eido/validate/main.nf index 798d3a05bf9..9346323e51c 100644 --- a/modules/nf-core/eido/validate/main.nf +++ b/modules/nf-core/eido/validate/main.nf @@ -3,7 +3,7 @@ process EIDO_VALIDATE { label 'process_single' conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' : 'biocontainers/eido:0.1.9_cv2' }" diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 5ca288bc3fe..fd4f90a7458 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -3,9 +3,9 @@ process ELPREP_FILTER { label 'process_high' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - 'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index d5ffc4973f5..ed4a43a314d 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -3,9 +3,9 @@ process ELPREP_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - 'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 639944ef3ee..f6eac485321 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -3,9 +3,9 @@ process ELPREP_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - 'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 0eb9514b520..431ea6363c8 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -3,9 +3,9 @@ process EMBOSS_SEQRET { label 'process_single' conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/emboss:6.6.0--hf657eab_5': - 'quay.io/biocontainers/emboss:6.6.0--h440b012_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/emboss:6.6.0--h440b012_4" } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 955cc308587..dc320ce0518 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -3,9 +3,9 @@ process EMMTYPER { label 'process_low' conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0' : - 'quay.io/biocontainers/emmtyper:0.2.0--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/emmtyper:0.2.0--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 73bdd293e29..3a52ba0c963 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -3,9 +3,9 @@ process ENDORSPY { label 'process_low' conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/endorspy:0.4--hdfd78af_0': - 'quay.io/biocontainers/endorspy:0.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/endorspy:0.4--hdfd78af_0" } input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index fd2c893aa73..22d80ba9e9b 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -3,9 +3,9 @@ process ENSEMBLVEP { label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' : - 'quay.io/biocontainers/ensembl-vep:106.1--pl5321h4a94de4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ensembl-vep:106.1--pl5321h4a94de4_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index e89289e9819..751e72506b9 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -3,9 +3,9 @@ process ENTREZDIRECT_ESEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), val(term) diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index d8b6e7b9b08..1e5c9138b6c 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -3,9 +3,9 @@ process ENTREZDIRECT_ESUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), val(uid), path(uids_file) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index 1b481063fcb..bcd7739d8b2 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -3,9 +3,9 @@ process ENTREZDIRECT_XTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), path(xml_input) diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index 6e0c348c6b8..5f518271298 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -3,9 +3,9 @@ process EPANG { label 'process_high' conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': - 'quay.io/biocontainers/epa-ng:0.3.8--h9a82719_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/epa-ng:0.3.8--h9a82719_1" } input: tuple val(meta), path(queryaln) diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index f60b75b48bd..c5bb63aeee4 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -3,9 +3,9 @@ process EXPANSIONHUNTER { label 'process_low' conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0' : - 'quay.io/biocontainers/expansionhunter:4.0.2--he785bd8_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/expansionhunter:4.0.2--he785bd8_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index 24f81a95156..879a47e9f10 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -3,9 +3,9 @@ process FAQCS { label 'process_medium' conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/faqcs%3A2.10--r41h9a82719_2' : - 'quay.io/biocontainers/faqcs:2.10--r41h9a82719_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/faqcs:2.10--r41h9a82719_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index dd82e8ce33d..efba5b48dc6 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -4,9 +4,9 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : - 'quay.io/biocontainers/fargene:0.1--py27h21c881e_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fargene:0.1--py27h21c881e_4" } input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index e6b44a8296f..fe61c7852e1 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -3,9 +3,9 @@ process FASTANI { label 'process_medium' conda (params.enable_conda ? "bioconda::fastani=1.32" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0' : - 'quay.io/biocontainers/fastani:1.32--he1c1bb9_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fastani:1.32--he1c1bb9_0" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index d25573fd703..cdf6b80e9d9 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -3,9 +3,9 @@ process FASTAWINDOWS { label 'process_low' conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0': - 'quay.io/biocontainers/fasta_windows:0.2.4--hec16e2b_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fasta_windows:0.2.4--hec16e2b_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 11ea4db32a6..d3f30095228 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -3,9 +3,9 @@ process FASTP { label 'process_medium' conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fastp:0.23.2--h79da9fb_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 05730368b2d..e26f1c307a1 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -3,9 +3,9 @@ process FASTQC { label 'process_medium' conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fastqc:0.11.9--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index 4cca0317e38..272f5da4fc1 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -3,9 +3,9 @@ process FASTQSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastq-scan:0.4.4--h7d875b9_0' : - 'quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fastq-scan:0.4.4--h7d875b9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index ce65846a6c9..1f0087ebe86 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -2,9 +2,9 @@ process FASTTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' : - 'quay.io/biocontainers/fasttree:2.1.10--h516909a_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fasttree:2.1.10--h516909a_4" } input: path alignment diff --git a/modules/nf-core/fcs/fcsadaptor/main.nf b/modules/nf-core/fcs/fcsadaptor/main.nf index 2a0afb5bb7b..3f2fed41f8d 100644 --- a/modules/nf-core/fcs/fcsadaptor/main.nf +++ b/modules/nf-core/fcs/fcsadaptor/main.nf @@ -6,7 +6,7 @@ process FCS_FCSADAPTOR { exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers." } // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif': 'ncbi/fcs-adaptor:0.2.3' }" diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index be7c56c23c6..d30e7c4c795 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -3,9 +3,9 @@ process FFQ { label 'process_low' conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0': - 'quay.io/biocontainers/ffq:0.2.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ffq:0.2.1--pyhdfd78af_0" } input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 88c5ab4c1a9..a960f825348 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -3,9 +3,9 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index a3279491cf3..287920c2116 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -3,9 +3,9 @@ process FGBIO_FASTQTOBAM { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 3014355c4f7..36ab0eca210 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -3,9 +3,9 @@ process FGBIO_GROUPREADSBYUMI { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(taggedbam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index bb718d0b8cd..6c9250e8067 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -3,9 +3,9 @@ process FGBIO_SORTBAM { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 1389c8aab5f..7828ad02521 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -3,9 +3,9 @@ process FGBIO_ZIPPERBAMS { label 'process_single' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(unmapped_bam) diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index afaa9382878..74c5839d7b3 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -3,9 +3,9 @@ process FILTLONG { label 'process_low' conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : - 'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/filtlong:0.2.1--h9a82719_0" } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index bb6f249970b..214608f34c6 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -2,9 +2,9 @@ process FLASH { tag "$meta.id" label 'process_medium' - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' : - 'quay.io/biocontainers/flash:1.2.11--hed695b0_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/flash:1.2.11--hed695b0_5" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 61d88fcb9f9..156aee43339 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -3,9 +3,9 @@ process FLYE { label 'process_high' conda (params.enable_conda ? "bioconda::flye=2.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' : - 'quay.io/biocontainers/flye:2.9--py39h6935b12_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/flye:2.9--py39h6935b12_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index b36fcadc86a..94a2ada46dd 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -3,9 +3,9 @@ process FQ_LINT { label 'process_low' conda (params.enable_conda ? "bioconda::fq=0.9.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': - 'quay.io/biocontainers/fq:0.9.1--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/fq:0.9.1--h9ee0642_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 73b1da961cf..19ed5b56705 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -3,9 +3,9 @@ process FREEBAYES { label 'process_low' conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3' : - 'quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/freebayes:1.3.5--py38ha193a2f_3" } input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 5c580df591f..980f2600b53 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -5,9 +5,9 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0': - 'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gamma:2.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 9cee804eedd..86652978380 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -3,9 +3,9 @@ process GAPPA_EXAMINEASSIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - 'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 24e334183c8..e35a9f9beb1 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -3,9 +3,9 @@ process GAPPA_EXAMINEGRAFT { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - 'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 9b9b56e1e01..11dc37a1a0d 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -3,9 +3,9 @@ process GAPPA_EXAMINEHEATTREE { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - 'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index bfe444e26b8..355d1b57a3c 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -3,9 +3,9 @@ process GATK_INDELREALIGNER { label 'process_single' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - 'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index ba6a25921f2..d467cf0d38d 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -3,9 +3,9 @@ process GATK_REALIGNERTARGETCREATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - 'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index e88ac7c5ae7..7d839d8c790 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -3,9 +3,9 @@ process GATK_UNIFIEDGENOTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - 'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index a0e2c45ca04..58bbc212cc3 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -3,9 +3,9 @@ process GATK4_APPLYBQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index d3da8332131..2685f41244f 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -3,9 +3,9 @@ process GATK4_APPLYVQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index fb26d3da73f..0fc04f6114f 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -3,9 +3,9 @@ process GATK4_BASERECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 6224d9b339f..e773bbbaac0 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -3,9 +3,9 @@ process GATK4_BEDTOINTERVALLIST { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index c289684edb7..4f9dc40f492 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -3,9 +3,9 @@ process GATK4_CALCULATECONTAMINATION { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 6e6d955a440..66990843cb8 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -3,9 +3,9 @@ process GATK4_CALIBRATEDRAGSTRMODEL { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index ed64d931a24..0a678189d5f 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -3,9 +3,9 @@ process GATK4_COLLECTREADCOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 5aac95a69b8..4aafd8d68e0 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -3,9 +3,9 @@ process GATK4_COLLECTSVEVIDENCE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index db4d9cdbaf7..b1f83361e1d 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -3,9 +3,9 @@ process GATK4_COMBINEGVCFS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 8f2f00f2bab..32197c7a790 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -3,9 +3,9 @@ process GATK4_COMPOSESTRTABLEFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 13fa9e81006..a21cfd3a049 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -3,9 +3,9 @@ process GATK4_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 653a949724f..58b93623e6c 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -3,9 +3,9 @@ process GATK4_CREATESOMATICPANELOFNORMALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 46e09a95bbb..2d951b7a440 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -3,9 +3,9 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 326d4d58d86..f1de0350c61 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -3,9 +3,9 @@ process GATK4_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 71de16f6d4b..b10deb59956 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -3,9 +3,9 @@ process GATK4_FILTERMUTECTCALLS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 98e620e7a6f..00caac2ecef 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -3,9 +3,9 @@ process GATK4_FILTERVARIANTTRANCHES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 231bd39e6ab..052022bedb6 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -3,9 +3,9 @@ process GATK4_GATHERBQSRREPORTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 0b763f4169a..b0e2593a376 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -3,9 +3,9 @@ process GATK4_GATHERPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 810f2b63b1e..e218fbd7f45 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -3,9 +3,9 @@ process GATK4_GENOMICSDBIMPORT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 11024b1b232..a380f03cb72 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -3,9 +3,9 @@ process GATK4_GENOTYPEGVCFS { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 5945a937ad6..60585af10ed 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -3,9 +3,9 @@ process GATK4_GETPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 19cd57bbf08..538f6cbe20a 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -3,9 +3,9 @@ process GATK4_HAPLOTYPECALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 264f71ef979..a0994768d74 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -3,9 +3,9 @@ process GATK4_INDEXFEATUREFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 84f3c472ea0..2067aa642a8 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -3,9 +3,9 @@ process GATK4_INTERVALLISTTOBED { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 7ab26c159e3..8dbd3f9470a 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -3,9 +3,9 @@ process GATK4_INTERVALLISTTOOLS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 8c4ac94e6f0..c472a2e4b30 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -3,9 +3,9 @@ process GATK4_LEARNREADORIENTATIONMODEL { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 1e3b80629a9..e2e0d8e4676 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -3,9 +3,9 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 63805c929d8..349c681aa0b 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -3,9 +3,9 @@ process GATK4_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index ff51de065a5..02435f7288d 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -3,9 +3,9 @@ process GATK4_MERGEBAMALIGNMENT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 54311df7f5a..cf7de937a38 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -3,9 +3,9 @@ process GATK4_MERGEMUTECTSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index c1ec942ec27..6fd8d1a6887 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -3,9 +3,9 @@ process GATK4_MERGEVCFS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index abec0d73d33..93ac3598979 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -3,9 +3,9 @@ process GATK4_MUTECT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 64c7279672d..d3b35f81e6d 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -3,9 +3,9 @@ process GATK4_PRINTSVEVIDENCE { label 'process_single' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 5640e8aef54..3957f841b29 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -3,9 +3,9 @@ process GATK4_REBLOCKGVCF { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 959c3e79ead..85f6dbfdd3f 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -3,9 +3,9 @@ process GATK4_REVERTSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index de83293ae97..1c11196f684 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -3,9 +3,9 @@ process GATK4_SAMTOFASTQ { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 633c21f2fe1..a49377b12cb 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -3,9 +3,9 @@ process GATK4_SELECTVARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index 9df66c21f58..56928a45b13 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -3,9 +3,9 @@ process GATK4_SPLITINTERVALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 456ec055565..eb02bacef09 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -3,9 +3,9 @@ process GATK4_SPLITNCIGARREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index cda06e1159a..f6ecc3be40c 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -3,9 +3,9 @@ process GATK4_VARIANTFILTRATION { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 961e60d8ef6..ac6404ff1b5 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -3,9 +3,9 @@ process GATK4_VARIANTRECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index 7bce527a0fc..4da15f4d4f1 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -3,9 +3,9 @@ process GECCO_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gecco:0.9.2--pyhdfd78af_0': - 'quay.io/biocontainers/gecco:0.9.2--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gecco:0.9.2--pyhdfd78af_0" } input: tuple val(meta), path(input), path(hmm) diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 0e30dc316f1..7d9c2fcc837 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -3,9 +3,9 @@ process GENMAP_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : - 'quay.io/biocontainers/genmap:1.3.0--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index 36c54c1c397..c095a1cb5da 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -3,9 +3,9 @@ process GENMAP_MAPPABILITY { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : - 'quay.io/biocontainers/genmap:1.3.0--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index b7ecd3fcb17..c3addf98d3a 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -3,9 +3,9 @@ process GENMOD_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - 'quay.io/biocontainers/genmod:3.7.4--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 4bdff8df899..7090b2f2d19 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -3,9 +3,9 @@ process GENMOD_COMPOUND { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - 'quay.io/biocontainers/genmod:3.7.4--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index d786d2695f9..5d74ce83d65 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -3,9 +3,9 @@ process GENMOD_MODELS { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - 'quay.io/biocontainers/genmod:3.7.4--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 9b7bd009858..2dcd229843b 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -3,9 +3,9 @@ process GENMOD_SCORE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - 'quay.io/biocontainers/genmod:3.7.4--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index 2ddf9e430dd..3f9d42642fc 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -3,9 +3,9 @@ process GENOMESCOPE2 { label 'process_low' conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': - 'quay.io/biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genomescope2:2.0--py310r41hdfd78af_5" } input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index 83da02bed11..d2ee076a29d 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -3,9 +3,9 @@ process GENOTYPHI_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1': - 'quay.io/biocontainers/genotyphi:1.9.1--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genotyphi:1.9.1--hdfd78af_1" } input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index d276c410780..0dcf3db28af 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -3,9 +3,9 @@ process GENRICH { label 'process_high' conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' : - 'quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/genrich:0.6.1--h5bf99c6_1" } input: tuple val(meta), path(treatment_bam) diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index 3ae5ad66265..cc9825553ff 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -4,9 +4,9 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' : - 'quay.io/biocontainers/gfaffix:0.1.4--hec16e2b_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gfaffix:0.1.4--hec16e2b_0" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 7c575c97ff2..772483ca956 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -3,9 +3,9 @@ process GFFREAD { label 'process_low' conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : - 'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gffread:0.12.1--h8b12597_0" } input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index b22370ca2bb..aa635f6cf19 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -3,9 +3,9 @@ process GLIMPSE_CHUNK { label 'process_medium' conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2': - 'quay.io/biocontainers/glimpse-bio:1.1.1--hce55b13_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/glimpse-bio:1.1.1--hce55b13_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index a26ab4cee5b..e809d0e7fd6 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -3,9 +3,9 @@ process GLNEXUS { label 'process_medium' conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : - 'quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/glnexus:1.4.1--h40d77a6_0" } input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index 3f8e4411875..8ca9037f83f 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -3,9 +3,9 @@ process GOAT_TAXONSEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0': - 'quay.io/biocontainers/goat:0.2.0--h92d785c_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/goat:0.2.0--h92d785c_0" } input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index 8834cc0ab66..a8e84257c56 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -4,9 +4,9 @@ process GRAPHMAP2_ALIGN { tag "$meta.id" conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : - 'quay.io/biocontainers/graphmap:0.6.3--he513fc3_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index ef240b6c05a..954434361d9 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -2,9 +2,9 @@ process GRAPHMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : - 'quay.io/biocontainers/graphmap:0.6.3--he513fc3_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index 36d8a311e02..1356ceddb9a 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -3,9 +3,9 @@ process GSTAMA_COLLAPSE { label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : - 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 9723d8f9ad1..4ac3e5bc66f 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -3,9 +3,9 @@ process GSTAMA_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' : - 'quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gs-tama:1.0.2--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index 214e5f936d1..f388d4bc9dc 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -3,9 +3,9 @@ process GSTAMA_POLYACLEANUP { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0': - 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 02ea970a489..743ca09dc3b 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -4,9 +4,9 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' : - 'quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gtdbtk:1.5.0--pyhdfd78af_0" } input: tuple val(meta), path("bins/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 17a271d8f76..5229c0b2689 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -2,9 +2,9 @@ process GUBBINS { label 'process_medium' conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : - 'quay.io/biocontainers/gubbins:3.0.0--py39h5bf99c6_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gubbins:3.0.0--py39h5bf99c6_0" } input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 04d4ce9f99c..7d17311a57a 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -3,9 +3,9 @@ process GUNC_DOWNLOADDB { label 'process_single' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : - 'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index ce9bd7c67c2..41cfac09373 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -3,9 +3,9 @@ process GUNC_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : - 'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index fa6ba26a578..e6768977778 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -3,7 +3,7 @@ process GUNZIP { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index 85794fbe832..c8df978af71 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -3,9 +3,9 @@ process GVCFTOOLS_EXTRACTVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gvcftools:0.17.0--he941832_3': - 'quay.io/biocontainers/gvcftools:0.17.0--he941832_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/gvcftools:0.17.0--he941832_3" } input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 32dacda06cb..96abdb14d91 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -3,9 +3,9 @@ process HAMRONIZATION_ABRICATE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index 815defcca7e..bc487074fc0 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -3,9 +3,9 @@ process HAMRONIZATION_AMRFINDERPLUS { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 467dd7cef58..3cbd143deec 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -3,9 +3,9 @@ process HAMRONIZATION_DEEPARG { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index b7d5dc64540..c125cf3ff34 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -3,9 +3,9 @@ process HAMRONIZATION_FARGENE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index c26ee7a890d..501a0fbeab1 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -3,9 +3,9 @@ process HAMRONIZATION_RGI { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index 2b58c30d456..06ad27c9347 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -2,9 +2,9 @@ process HAMRONIZATION_SUMMARIZE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: path(reports) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index 08c1c76bf50..69a3029df39 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -3,9 +3,9 @@ process HAPLOCHECK { label 'process_low' conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': - 'quay.io/biocontainers/haplocheck:1.3.3--h4a94de4_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/haplocheck:1.3.3--h4a94de4_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index c49cb957344..8e6e3e4774e 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -3,9 +3,9 @@ process HAPLOGREP2_CLASSIFY { label 'process_low' conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/haplogrep:2.4.0--hdfd78af_0': - 'quay.io/biocontainers/haplogrep:2.4.0--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/haplogrep:2.4.0--hdfd78af_0" } input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index c972a7417c6..65cc0d88151 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -4,9 +4,9 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - 'quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index e2e42c67614..c4eb79716f8 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -4,9 +4,9 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - 'quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } input: tuple val(meta), path(vcf), path(bed) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 51fe0b83db7..47f53419002 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -3,9 +3,9 @@ process HICAP { label 'process_low' conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' : - 'quay.io/biocontainers/hicap:1.0.3--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hicap:1.0.3--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index ea7c4976d2a..a3458661157 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -3,9 +3,9 @@ process HIFIASM { label 'process_high' conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' : - 'quay.io/biocontainers/hifiasm:0.15.4--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hifiasm:0.15.4--h2e03b76_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index a6f81a6c833..b165406df29 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -4,9 +4,9 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : - 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index fee4064ce84..81651baed38 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -5,9 +5,9 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : - 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } input: path fasta diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 1423f25cd29..f683efd9fa0 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -4,9 +4,9 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : - 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 4a2f9fedbeb..8640e7d6ab0 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -3,9 +3,9 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : - 'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 9c9431c72eb..01df3607e6b 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -4,9 +4,9 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': - 'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 196d036bf43..62eaedd2de8 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -3,9 +3,9 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': - 'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 95a02a6752d..71d9b2746ba 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -4,9 +4,9 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : - 'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index fb6cbe8aaec..0996adea5f5 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -3,9 +3,9 @@ process HMMER_ESLALIMASK { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 464a51d0df3..f6bfe7fee90 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -3,9 +3,9 @@ process HMMER_ESLREFORMAT { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index afa59a26044..21a2fb32640 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -3,9 +3,9 @@ process HMMER_HMMALIGN { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 802dd7ebffd..02b50736fe9 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -3,9 +3,9 @@ process HMMER_HMMBUILD { label 'process_low' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2': - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 3a2d15b7f7a..4d81d4ad7ec 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -3,9 +3,9 @@ process HMMER_HMMSEARCH { label 'process_medium' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index a17969248b8..d05229644ca 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -3,9 +3,9 @@ process HMTNOTE { label 'process_low' conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0': - 'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hmtnote:0.7.2--pyhdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 9056a5ab50e..42ec3f4c108 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -4,9 +4,9 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 29a08c69009..23c630ce612 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -4,9 +4,9 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index d679b0cf1e2..d2014cd1392 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,9 +5,9 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' : - 'quay.io/biocontainers/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 7ef58b3d6b8..854d35dd3e3 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -4,9 +4,9 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index f0a2ee2165b..12873c7dbb8 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -4,9 +4,9 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 39210430b35..2634dab91a6 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -4,9 +4,9 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0': - 'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hpsuissero:1.0.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index 976eb3d8e98..47371a78d7a 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -3,9 +3,9 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : - 'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } input: path wigs diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index fb52166d0e3..62b268bebca 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -4,9 +4,9 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : - 'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index d18ef2ebc51..58370ef9600 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -3,9 +3,9 @@ process IDR { label 'process_low' conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : - 'quay.io/biocontainers/idr:2.0.4.2--py39hcbe4a3b_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/idr:2.0.4.2--py39hcbe4a3b_5" } input: path peaks diff --git a/modules/nf-core/imputeme/vcftoprs/main.nf b/modules/nf-core/imputeme/vcftoprs/main.nf index 8ce3f73d03b..4abc12bc156 100644 --- a/modules/nf-core/imputeme/vcftoprs/main.nf +++ b/modules/nf-core/imputeme/vcftoprs/main.nf @@ -3,7 +3,7 @@ process IMPUTEME_VCFTOPRS { label 'process_low' conda (params.enable_conda ? "YOUR-TOOL-HERE" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img' : 'biocontainers/imputeme:vv1.0.7_cv1' }" diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index 74e4b3ab207..8138a66b9f9 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -3,9 +3,9 @@ process INSTRAIN_PROFILE { label 'process_high' conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0': - 'quay.io/biocontainers/instrain:1.6.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/instrain:1.6.1--pyhdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index db394bd2897..decb4d34fa6 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -3,9 +3,9 @@ process IQTREE { label 'process_medium' conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' : - 'quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/iqtree:2.1.4_beta--hdcc8f71_0" } input: path alignment diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index a2c79115849..4e3599aa902 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -3,9 +3,9 @@ process ISMAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' : - 'quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ismapper:2.0.2--pyhdfd78af_1" } input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index fe1b10d4ae3..27c69b918d4 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -3,9 +3,9 @@ process ISOSEQ3_CLUSTER { label 'process_medium' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : - 'quay.io/biocontainers/isoseq3:3.4.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index f65cac2a161..393a2ffeb7a 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -3,9 +3,9 @@ process ISOSEQ3_REFINE { label 'process_low' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : - 'quay.io/biocontainers/isoseq3:3.4.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index db6301e9066..e33580097fb 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -3,9 +3,9 @@ process IVAR_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index 819aa5dd103..0cc40d92704 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -3,9 +3,9 @@ process IVAR_TRIM { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index b86042f05fd..bab663e9c16 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -3,9 +3,9 @@ process IVAR_VARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index baed502c371..08dd08837bf 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -8,9 +8,9 @@ process JUPYTERNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' : - 'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index ae8f99e6022..0fb8ca4c660 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -3,9 +3,9 @@ process KAIJU_KAIJU { label 'process_high' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - 'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 3f35ce7ee31..20c3160a4e7 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -3,9 +3,9 @@ process KAIJU_KAIJU2KRONA { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - 'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 8648d561d22..9b0c29959d1 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -3,9 +3,9 @@ process KAIJU_KAIJU2TABLE { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - 'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h2e03b76_0" } input: tuple val(meta), path(results) diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 8b25b7e2867..9c5773c5729 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -3,9 +3,9 @@ process KALLISTO_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - 'quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kallisto:0.46.2--h4f7b962_1" } input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 52accd3195f..0a350d71ccd 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -3,9 +3,9 @@ process KALLISTOBUSTOOLS_COUNT { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - 'quay.io/biocontainers/kb-python:0.27.2--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 89943ec96c1..7d00cd8b942 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -3,9 +3,9 @@ process KALLISTOBUSTOOLS_REF { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - 'quay.io/biocontainers/kb-python:0.27.2--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } input: path fasta diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index e9a486f904c..29cf554d8cb 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -3,9 +3,9 @@ process KAT_HIST { label 'process_medium' conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2': - 'quay.io/biocontainers/kat:2.4.2--py38hfc5f9d8_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kat:2.4.2--py38hfc5f9d8_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index f89b2585b6e..ce97648961b 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -3,9 +3,9 @@ process KHMER_NORMALIZEBYMEDIAN { label 'process_long' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : - 'quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } input: path pe_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 8ad89a6287b..d04df729865 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -3,9 +3,9 @@ process KHMER_UNIQUEKMERS { label 'process_low' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : - 'quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } input: path fasta diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index 88cbc951b91..29a6f2393f8 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -3,9 +3,9 @@ process KLEBORATE { label 'process_medium' conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' : - 'quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/kleborate:2.1.0--pyhdfd78af_1" } input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 43a167916a2..980b34723fd 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -3,9 +3,9 @@ process KRAKEN2_KRAKEN2 { label 'process_high' conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : - 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index fdcc2459855..488c91dbaeb 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,9 +2,9 @@ process KRAKENTOOLS_COMBINEKREPORTS { label 'process_single' conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': - 'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 8ed46f1327c..9befeec29a2 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -4,9 +4,9 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': - 'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index 88fe24f7e30..278270bfcfe 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -4,9 +4,9 @@ process KRONA_KRONADB { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : - 'quay.io/biocontainers/krona:2.7.1--pl526_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 79c01d71cb1..cb6b4496089 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -4,9 +4,9 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : - 'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.8--pl5262hdfd78af_2" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index edf7aab64d9..463c53df5d0 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -3,9 +3,9 @@ process KRONA_KTIMPORTTEXT { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': - 'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.8.1--pl5321hdfd78af_1" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index ef51a291397..16cd3d01e19 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -4,9 +4,9 @@ process KRONA_KTUPDATETAXONOMY { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : - 'quay.io/biocontainers/krona:2.7.1--pl526_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index a71d001aea1..614f50cf423 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -3,9 +3,9 @@ process LAST_DOTPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 882b16cd0f2..a3d25770b2a 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -3,9 +3,9 @@ process LAST_LASTAL { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 0747ba4dc06..b0e282180d1 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -3,9 +3,9 @@ process LAST_LASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 8ffec2f9228..57a92cde5df 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -3,9 +3,9 @@ process LAST_MAFCONVERT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 55f6a1a9693..cad83b254ca 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -3,9 +3,9 @@ process LAST_MAFSWAP { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 6bc649303f7..6333ca8b38f 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -3,9 +3,9 @@ process LAST_POSTMASK { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 433eff0c49b..a8870ccf093 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -3,9 +3,9 @@ process LAST_SPLIT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 23f4f36bd35..bc5b1ed480c 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -3,9 +3,9 @@ process LAST_TRAIN { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - 'quay.io/biocontainers/last:1250--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index aa11fe03427..b4e6f634f15 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -4,9 +4,9 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' : - 'quay.io/biocontainers/leehom:1.2.15--h29e30f7_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/leehom:1.2.15--h29e30f7_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index 8e2a3ae3cc8..a406b47d401 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -3,9 +3,9 @@ process LEGSTA { label 'process_medium' conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2': - 'quay.io/biocontainers/legsta:0.5.1--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/legsta:0.5.1--hdfd78af_2" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 3c6b87999a4..10fe343ee06 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -3,9 +3,9 @@ process LIMA { label 'process_low' conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' : - 'quay.io/biocontainers/lima:2.2.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/lima:2.2.0--h9ee0642_0" } input: tuple val(meta), path(ccs) diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index 29995db8307..e33dce314be 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -3,9 +3,9 @@ process LISSERO { label 'process_low' conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0' : - 'quay.io/biocontainers/lissero:0.4.9--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/lissero:0.4.9--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index 773bc21244b..d67a92ec40e 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -3,9 +3,9 @@ process LOFREQ_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 4dffc302a9e..6502ad20beb 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -3,9 +3,9 @@ process LOFREQ_CALLPARALLEL { label 'process_high' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index bddc012f8fd..bc7be19a6e7 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -3,9 +3,9 @@ process LOFREQ_FILTER { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index ac53d70fc7e..12717f8b387 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -3,9 +3,9 @@ process LOFREQ_INDELQUAL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 65db4d3e8e0..5a540eb0b86 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -3,9 +3,9 @@ process MACREL_CONTIGS { label 'process_medium' conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0': - 'quay.io/biocontainers/macrel:1.1.0--py36hc5360cc_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/macrel:1.1.0--py36hc5360cc_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 9aaf97a93be..50198829160 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -3,9 +3,9 @@ process MACS2_CALLPEAK { label 'process_medium' conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' : - 'quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/macs2:2.2.7.1--py38h4a8c8d9_3" } input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 99485b61d7b..da92735711e 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -3,9 +3,9 @@ process MAFFT { label 'process_high' conda (params.enable_conda ? "bioconda::mafft=7.490" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0': - 'quay.io/biocontainers/mafft:7.490--h779adbc_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mafft:7.490--h779adbc_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 7fa990c0673..7ba57002bb0 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -3,9 +3,9 @@ process MALT_BUILD { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : - 'quay.io/biocontainers/malt:0.41--1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/malt:0.41--1" } input: path fastas diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index 2b91d90584e..03dbc3fbb37 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -3,9 +3,9 @@ process MALT_RUN { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : - 'quay.io/biocontainers/malt:0.41--1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/malt:0.41--1" } input: tuple val(meta), path(fastqs) diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index 75710141780..d24ac92c450 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -3,9 +3,9 @@ process MALTEXTRACT { label 'process_medium' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : - 'quay.io/biocontainers/hops:0.35--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } input: path rma6 diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index c38fd2545be..95b87008263 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -3,9 +3,9 @@ process MANTA_CONVERTINVERSION { label 'process_low' conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0': - 'quay.io/biocontainers/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 5f2964fbd01..cdbf38e5da1 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -3,9 +3,9 @@ process MANTA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 0b40965b7c2..bbd3e3129d5 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -3,9 +3,9 @@ process MANTA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 759f9cb9ec5..8366a83f93d 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -3,9 +3,9 @@ process MANTA_TUMORONLY { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index b454b0a0add..402f292a2bf 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -3,9 +3,9 @@ process MAPDAMAGE2 { label 'process_single' conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' : - 'quay.io/biocontainers/mapdamage2:2.2.1--pyr40_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mapdamage2:2.2.1--pyr40_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index 270767b5682..a044d569750 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -3,9 +3,9 @@ process MASH_DIST { label 'process_low' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : - 'quay.io/biocontainers/mash:2.3--he348c14_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index be272cbb105..913a93679cf 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -3,9 +3,9 @@ process MASH_SCREEN { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1': - 'quay.io/biocontainers/mash:2.3--he348c14_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 54263af775d..3a875aa7ad3 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -2,9 +2,9 @@ process MASH_SKETCH { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : - 'quay.io/biocontainers/mash:2.3--he348c14_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index 4cd9af1929e..bd40dcfcd97 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -3,9 +3,9 @@ process MASHTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' : - 'quay.io/biocontainers/mashtree:1.2.0--pl526h516909a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mashtree:1.2.0--pl526h516909a_0" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index a48df43fd7a..d001a66be44 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -3,9 +3,9 @@ process MAXBIN2 { label 'process_medium' conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' : - 'quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/maxbin2:2.2.7--he1b5a44_2" } input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index 3fc45725352..2bf0f411986 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -5,7 +5,7 @@ process MAXQUANT_LFQ { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" } else { - container "quay.io/biocontainers/maxquant:2.0.3.0--py310hdfd78af_1" + container ${params.docker_url ?: 'quay.io/biocontainers'}/maxquant:2.0.3.0--py310hdfd78af_1 } input: diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index e1f4b92df2e..62d0eaca2e1 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -4,9 +4,9 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0': - 'quay.io/biocontainers/mcroni:1.0.4--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mcroni:1.0.4--pyh5e36f6f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index c8d505a14ae..a9ccd61785a 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -3,7 +3,7 @@ process MD5SUM { label 'process_single' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index da77d0f0d41..561d71d4cd0 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -3,9 +3,9 @@ process MEDAKA { label 'process_high' conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' : - 'quay.io/biocontainers/medaka:1.4.4--py38h130def0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/medaka:1.4.4--py38h130def0_0" } input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 6e6a1ad1030..1017c51eda8 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -3,9 +3,9 @@ process MEGAHIT { label 'process_high' conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' : - 'quay.io/biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index ac499a0c5a5..414ef622fa7 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -3,9 +3,9 @@ process MEGAN_DAA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - 'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } input: tuple val(meta), path(daa) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 9c6a094b688..aaf10074064 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -3,9 +3,9 @@ process MEGAN_RMA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - 'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index 24c3002956a..452538efedc 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -3,9 +3,9 @@ process MENINGOTYPE { label 'process_low' conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0' : - 'quay.io/biocontainers/meningotype:0.8.5--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/meningotype:0.8.5--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index 4b2d87cef79..2cf7eb2ce7a 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -3,9 +3,9 @@ process MERQURY { label 'process_low' conda (params.enable_conda ? "bioconda::merqury=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1': - 'quay.io/biocontainers/merqury:1.3--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/merqury:1.3--hdfd78af_1" } input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index f7a2811ddd2..8485e228396 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -3,9 +3,9 @@ process MERYL_COUNT { label 'process_medium' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - 'quay.io/biocontainers/meryl:1.3--h87f3376_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index a1f18f0589e..5a8bd2b09d5 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -3,9 +3,9 @@ process MERYL_HISTOGRAM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - 'quay.io/biocontainers/meryl:1.3--h87f3376_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 98baa870112..53084f80bf6 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -3,9 +3,9 @@ process MERYL_UNIONSUM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - 'quay.io/biocontainers/meryl:1.3--h87f3376_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 7125eeb22eb..830d64c40da 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -3,9 +3,9 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : - 'quay.io/biocontainers/metabat2:2.15--h986a166_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 23ebe19a2dd..e11a516155e 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -3,9 +3,9 @@ process METABAT2_METABAT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : - 'quay.io/biocontainers/metabat2:2.15--h986a166_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 7c37ecab08e..221c8da6ad4 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,9 +2,9 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { label 'process_single' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : - 'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 1453466d72a..9a439967ccc 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -3,9 +3,9 @@ process METAPHLAN3_METAPHLAN3 { label 'process_high' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : - 'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index b42420734f4..49d35d02f6e 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -3,9 +3,9 @@ process METHYLDACKEL_EXTRACT { label 'process_medium' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - 'quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index 755e62f88c0..399c283205e 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -3,9 +3,9 @@ process METHYLDACKEL_MBIAS { label 'process_low' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - 'quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 87dd74f9aaa..a7344149370 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -3,9 +3,9 @@ process MINIA { label 'process_high' conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : - 'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/minia:3.2.6--h9a82719_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index f77b10f2225..8410aceb09e 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -3,9 +3,9 @@ process MINIASM { label 'process_high' conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' : - 'quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/miniasm:0.3_r179--h5bf99c6_2" } input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index 08ac6eeffe5..5fc0eede5cf 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -3,9 +3,9 @@ process MINIMAP2_ALIGN { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : - 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 25e942920bb..2e97c2af193 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -2,9 +2,9 @@ process MINIMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : - 'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/minimap2:2.21--h5bf99c6_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index ca86fba834f..0f2c6e4a8e5 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -3,9 +3,9 @@ process MLST { label 'process_low' conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : - 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mlst:2.19.0--hdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index 9ca7e180364..a434e841b71 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -3,9 +3,9 @@ process MOBSUITE_RECON { label 'process_medium' conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0': - 'quay.io/biocontainers/mob_suite:3.0.3--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mob_suite:3.0.3--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index d7e3c92904a..ecb8bc7a92f 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -3,9 +3,9 @@ process MOSDEPTH { label 'process_medium' conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : - 'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}" + "${params.docker_url ?: 'quay.io/biocontainers'}/mosdepth:0.3.3--hdfd78af_1"} input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index c60cb817af8..b461e45f6df 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -2,9 +2,9 @@ process MOTUS_DOWNLOADDB { label 'process_low' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - 'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index d9f091e16fe..de549938be9 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -5,9 +5,9 @@ process MOTUS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - 'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index bd7a127320d..61b088d47cc 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -3,9 +3,9 @@ process MOTUS_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - 'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index 954c5bec398..896ca71873f 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -3,9 +3,9 @@ process MSISENSOR_MSI { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : - 'quay.io/biocontainers/msisensor:0.5--hb3646a4_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index 399513cec88..520f90fc69b 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -3,9 +3,9 @@ process MSISENSOR_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : - 'quay.io/biocontainers/msisensor:0.5--hb3646a4_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index 130014b7f2f..a9864e71971 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -3,9 +3,9 @@ process MSISENSOR2_MSI { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': - 'quay.io/biocontainers/msisensor2:0.1--hd03093a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index 03cebbdb997..84a3c7f4e42 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -3,9 +3,9 @@ process MSISENSOR2_SCAN { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': - 'quay.io/biocontainers/msisensor2:0.1--hd03093a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } input: path fasta diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index e2da70de7c6..f0e7b3375e0 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -3,9 +3,9 @@ process MSISENSORPRO_MSI_SOMATIC { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - 'quay.io/biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index 752606d620f..bf358fb6008 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -3,9 +3,9 @@ process MSISENSORPRO_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - 'quay.io/biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index cf9f384a8d3..eb192bce027 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -3,9 +3,9 @@ process MTNUCRATIO { label 'process_single' conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' : - 'quay.io/biocontainers/mtnucratio:0.7--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mtnucratio:0.7--hdfd78af_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index a8159a57bf0..8675c2598ee 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -2,9 +2,9 @@ process MULTIQC { label 'process_single' conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 24e83335940..4595770b1a2 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -3,9 +3,9 @@ process MULTIVCFANALYZER { label 'process_single' conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multivcfanalyzer:0.85.2--hdfd78af_1': - 'quay.io/biocontainers/multivcfanalyzer:0.85.2--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/multivcfanalyzer:0.85.2--hdfd78af_1" } input: path vcfs diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index 746abbb1250..f8d21373a75 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -4,9 +4,9 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : - 'quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 50f3c3f47a9..4c3163f1129 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -3,9 +3,9 @@ process MUSCLE { label 'process_single' conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' : - 'quay.io/biocontainers/muscle:3.8.1551--h7d875b9_6' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/muscle:3.8.1551--h7d875b9_6" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index f5e2ccf271a..817b1cad2e9 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -3,9 +3,9 @@ process MYKROBE_PREDICT { label 'process_low' conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1': - 'quay.io/biocontainers/mykrobe:0.11.0--py39h2add14b_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mykrobe:0.11.0--py39h2add14b_1" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 2b4f0928aae..6daf39d3585 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -3,9 +3,9 @@ process NANOLYSE { label 'process_low' conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' : - 'quay.io/biocontainers/nanolyse:1.2.0--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/nanolyse:1.2.0--py_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index 83c0e2ecf78..79268beba64 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -3,9 +3,9 @@ process NANOPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' : - 'quay.io/biocontainers/nanoplot:1.40.0--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/nanoplot:1.40.0--pyhdfd78af_0" } input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index 7bc15997589..d8cd3cda3e0 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -3,9 +3,9 @@ process NCBIGENOMEDOWNLOAD { label 'process_low' conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.1--pyh5e36f6f_0' : - 'quay.io/biocontainers/ncbi-genome-download:0.3.1--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ncbi-genome-download:0.3.1--pyh5e36f6f_0" } input: val meta diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index a9f52c84f0f..6dbbae8d49b 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -3,9 +3,9 @@ process NEXTCLADE_DATASETGET { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : - 'quay.io/biocontainers/nextclade:2.2.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 22f72781e04..5d5ba228c99 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -3,9 +3,9 @@ process NEXTCLADE_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : - 'quay.io/biocontainers/nextclade:2.2.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index ad6194202ec..39690aae009 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -3,9 +3,9 @@ process NEXTGENMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextgenmap%3A0.5.5--hc9558a2_4' : - 'quay.io/biocontainers/nextgenmap:0.5.5--hc9558a2_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/nextgenmap:0.5.5--hc9558a2_4" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index ef288e8f564..bd3e4b5ea50 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -3,9 +3,9 @@ process NGMASTER { label 'process_low' conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1' : - 'quay.io/biocontainers/ngmaster:0.5.8--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ngmaster:0.5.8--pyhdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 0898cee8352..13aae5cdb13 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,9 +2,9 @@ process NGSCHECKMATE_NCM { label 'process_low' conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3': - 'quay.io/biocontainers/ngscheckmate:1.0.0--py27r41hdfd78af_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ngscheckmate:1.0.0--py27r41hdfd78af_3" } input: path files diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index 5b70abd9269..152a4dadffb 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -3,9 +3,9 @@ process NUCMER { label 'process_low' conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : - 'quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index b6a3e2000bb..27815fe5f69 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -3,9 +3,9 @@ process OPTITYPE { label 'process_medium' conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' : - 'quay.io/biocontainers/optitype:1.3.5--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/optitype:1.3.5--0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index 0b8c63c60fb..e3a171bd760 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -3,9 +3,9 @@ process PAIRIX { label 'process_medium' conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : - 'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairix:0.3.7--py36h30a8e3e_3" } input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 2c171e7a638..157c8f54655 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -3,9 +3,9 @@ process PAIRTOOLS_DEDUP { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 4959c4eef25..260ae3d54e8 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -3,9 +3,9 @@ process PAIRTOOLS_FLIP { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 190346b1353..8e31fe2234d 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -3,9 +3,9 @@ process PAIRTOOLS_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 59e18648c8b..0ca6f4178d6 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -3,9 +3,9 @@ process PAIRTOOLS_RESTRICT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(pairs) diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index 9d434884ed4..aa969b838dd 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -3,9 +3,9 @@ process PAIRTOOLS_SELECT { label 'process_medium' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index 15ed56d1a83..8fea7111cd8 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -3,9 +3,9 @@ process PAIRTOOLS_SORT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index d8be0c1e3bb..ed819d925c2 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -3,9 +3,9 @@ process PANAROO_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0': - 'quay.io/biocontainers/panaroo:1.2.9--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/panaroo:1.2.9--pyhdfd78af_0" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 6414b5d3657..fd630c28eb5 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -3,9 +3,9 @@ process PANGOLIN { label 'process_medium' conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : - 'quay.io/biocontainers/pangolin:4.1.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pangolin:4.1.1--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index dfc47d4810d..80a1a80ed6a 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -4,9 +4,9 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' : - 'quay.io/biocontainers/paraclu:10--h9a82719_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/paraclu:10--h9a82719_1" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 35aec31457d..3fb34d750f7 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -3,9 +3,9 @@ process PASTY { label 'process_single' conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pasty:1.0.0--hdfd78af_0': - 'quay.io/biocontainers/pasty:1.0.0--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pasty:1.0.0--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index aa0ca78882f..dd4635e4315 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -3,9 +3,9 @@ process PBBAM_PBMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' : - 'quay.io/biocontainers/pbbam:1.7.0--h058f120_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pbbam:1.7.0--h058f120_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 5bfae1bf31c..52ec2dbda91 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -3,9 +3,9 @@ process PBCCS { label 'process_low' conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' : - 'quay.io/biocontainers/pbccs:6.2.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pbccs:6.2.0--h9ee0642_0" } input: tuple val(meta), path(bam), path(pbi) diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 6d423cf22b3..86e7401017f 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -3,9 +3,9 @@ process PBPTYPER { label 'process_single' conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbptyper:1.0.2--hdfd78af_0': - 'quay.io/biocontainers/pbptyper:1.0.2--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pbptyper:1.0.2--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index 7569d611acd..44fdf8d991d 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -3,9 +3,9 @@ process PEAR { label 'process_low' conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pear:0.9.6--h67092d7_8': - 'quay.io/biocontainers/pear:0.9.6--h67092d7_8' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pear:0.9.6--h67092d7_8" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index 50cdc698349..d61ab718f22 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -3,9 +3,9 @@ process PEDDY { label 'process_low' conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : - 'quay.io/biocontainers/peddy:0.4.8--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/peddy:0.4.8--pyh5e36f6f_0" } input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 43fca683627..2ca314c84b5 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -4,9 +4,9 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' : - 'quay.io/biocontainers/phantompeakqualtools:1.2.2--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/phantompeakqualtools:1.2.2--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index 23c38d56cb6..c772e93d7c4 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -3,9 +3,9 @@ process PHYLOFLASH { label 'process_medium' conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1' : - 'quay.io/biocontainers/phyloflash:3.4--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/phyloflash:3.4--hdfd78af_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index f7f929dec3c..acfdaf5ee32 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -3,9 +3,9 @@ process PICARD_ADDORREPLACEREADGROUPS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 36b86502156..e0d2309ea75 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -3,9 +3,9 @@ process PICARD_CLEANSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 6cc04dbf398..85865a7d912 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -3,9 +3,9 @@ process PICARD_COLLECTHSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 63f4e872951..c39173d6d56 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -3,9 +3,9 @@ process PICARD_COLLECTMULTIPLEMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 2b0aeefefe2..d4483f2568d 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -3,9 +3,9 @@ process PICARD_COLLECTWGSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 0976f049360..1b70e32d943 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -3,9 +3,9 @@ process PICARD_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index d4eef2f2118..12581a4fc39 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -3,9 +3,9 @@ process PICARD_CROSSCHECKFINGERPRINTS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(input1) diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index 2feb274ca55..552933a1aec 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -3,9 +3,9 @@ process PICARD_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index fda978030f1..9c416217562 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -3,9 +3,9 @@ process PICARD_FILTERSAMREADS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index eea9eca92ab..7a488cafe7c 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -3,9 +3,9 @@ process PICARD_FIXMATEINFORMATION { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 334f68b0f89..7009bfee90f 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -3,9 +3,9 @@ process PICARD_LIFTOVERVCF { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index d1f3aaa1e79..3d63babcb5c 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -3,9 +3,9 @@ process PICARD_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index cccf4d3d53f..83a0d41af1f 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -3,9 +3,9 @@ process PICARD_MERGESAMFILES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index da492b0da53..ccba0c44447 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -4,9 +4,9 @@ process PICARD_RENAMESAMPLEINVCF { label 'process_single' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 759c2c3d9ef..5305e44b65f 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -3,9 +3,9 @@ process PICARD_SORTSAM { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index b57b39c62d0..faf2aac260e 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -3,9 +3,9 @@ process PICARD_SORTVCF { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index c7ab2ae0eef..db2191e3c19 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -3,9 +3,9 @@ process PINTS_CALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' : - 'quay.io/biocontainers/pypints:1.1.6--pyh5e36f6f_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pypints:1.1.6--pyh5e36f6f_1" } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index ebef5b37b4c..c71d1d22ec3 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -3,9 +3,9 @@ process PIRATE { label 'process_medium' conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' : - 'quay.io/biocontainers/pirate:1.0.4--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pirate:1.0.4--hdfd78af_2" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index 41a91dacf75..b286616303c 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -4,9 +4,9 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1': - 'quay.io/biocontainers/plasmidfinder:2.1.6--py310hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plasmidfinder:2.1.6--py310hdfd78af_1" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index 7911d806899..d47b0586c9a 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -3,9 +3,9 @@ process PLASMIDID { label 'process_medium' conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' : - 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plasmidid:1.6.5--hdfd78af_0" } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index fa22b527f5a..c9c22ae8192 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -3,9 +3,9 @@ process PLINK_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : - 'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index 0a69a021f74..edf94a0414b 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -3,9 +3,9 @@ process PLINK_VCF { label 'process_medium' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : - 'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index 15f9c0386d4..72cd40b600c 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -3,9 +3,9 @@ process PLINK2_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - 'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index 6f561322f29..b807d17e7fe 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -3,9 +3,9 @@ process PLINK2_SCORE { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - 'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(pgen), path(psam), path(pvar) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index 090851a8a26..ce2a48b0cd9 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -3,9 +3,9 @@ process PLINK2_VCF { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - 'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 2d9d6eb3e9d..3bb727fb775 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -3,9 +3,9 @@ process PMDTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5' : - 'quay.io/biocontainers/pmdtools:0.60--hdfd78af_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pmdtools:0.60--hdfd78af_5" } input: tuple val(meta), path(bam), path (bai) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index 77050bc7252..e9a54cb2f12 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -3,9 +3,9 @@ process PORECHOP { label 'process_medium' conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : - 'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/porechop:0.2.4--py39h7cff6ad_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 79ef66f55cd..1f58d2689a5 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -4,9 +4,9 @@ process PRESEQ_CCURVE { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - 'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index a98a922c01f..260651f5646 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -4,9 +4,9 @@ process PRESEQ_LCEXTRAP { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - 'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index ebd8c58c6ad..1fbdb2b33a6 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -3,9 +3,9 @@ process PRINSEQPLUSPLUS { label 'process_low' conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1': - 'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/prinseq-plus-plus:1.2.3--hc90279e_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 924a579ca60..4cb57f033fb 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -3,9 +3,9 @@ process PRODIGAL { label 'process_single' conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : - 'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index df52d29a915..6be25899cc8 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -3,9 +3,9 @@ process PROKKA { label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' : - 'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/prokka:1.14.6--pl5321hdfd78af_4" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index a5e6fcb2023..420567618c3 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -3,9 +3,9 @@ process PYCOQC { label 'process_medium' conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' : - 'quay.io/biocontainers/pycoqc:2.5.2--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pycoqc:2.5.2--py_0" } input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index 3463b0e5791..d23425dbc79 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -3,9 +3,9 @@ process PYDAMAGE_ANALYZE { label 'process_medium' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - 'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index c58d82f4124..a301a0a2184 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -3,9 +3,9 @@ process PYDAMAGE_FILTER { label 'process_single' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - 'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 4c75b00359e..5f00302561f 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -3,9 +3,9 @@ process QCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' : - 'quay.io/biocontainers/qcat:1.1.0--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/qcat:1.1.0--py_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 3bfcb4c1f58..dfb2a72d74e 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -3,9 +3,9 @@ process QUALIMAP_BAMQC { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - 'quay.io/biocontainers/qualimap:2.2.2d--1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index e136b8e24fb..4a3876c7a15 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -3,9 +3,9 @@ process QUALIMAP_BAMQCCRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' : - 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" } input: tuple val(meta), path(cram), path(crai) diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 38293d27f25..8f6714a3c2d 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -3,9 +3,9 @@ process QUALIMAP_RNASEQ { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - 'quay.io/biocontainers/qualimap:2.2.2d--1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index 5585491b1bc..7fa153a7748 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -2,9 +2,9 @@ process QUAST { label 'process_medium' conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : - 'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/quast:5.2.0--py39pl5321h2add14b_1" } input: path consensus diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index 6f8448967f9..8a0f9446406 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -3,9 +3,9 @@ process RACON { label 'process_high' conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' : - 'quay.io/biocontainers/racon:1.4.20--h9a82719_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/racon:1.4.20--h9a82719_1" } input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 7a06335bdee..35cdb758469 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -3,9 +3,9 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : - 'quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" } input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 47c8ece6179..5605e292c3b 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -3,9 +3,9 @@ process RASUSA { label 'process_low' conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1' : - 'quay.io/biocontainers/rasusa:0.3.0--h779adbc_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rasusa:0.3.0--h779adbc_1" } input: tuple val(meta), path(reads), val(genome_size) diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index 8bcf6bb1791..b8187eb5bbb 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -3,9 +3,9 @@ process RAVEN { label 'process_medium' conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/raven-assembler:1.6.1--h2e03b76_0' : - 'quay.io/biocontainers/raven-assembler:1.6.1--h2e03b76_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/raven-assembler:1.6.1--h2e03b76_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index e872a4e61ab..1760e2a6b40 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -2,9 +2,9 @@ process RAXMLNG { label 'process_high' conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' : - 'quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/raxml-ng:1.0.3--h32fcf60_0" } input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 711bf1c3ab3..459996af325 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -3,9 +3,9 @@ process RGI_MAIN { label 'process_medium' conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2': - 'quay.io/biocontainers/rgi:5.2.1--pyha8f3691_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rgi:5.2.1--pyha8f3691_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 95d647b1b26..df59e23a976 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -3,9 +3,9 @@ process RHOCALL_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - 'quay.io/biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rhocall:0.5.1--py39hbf8eff0_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 336b0af00f9..46eb80b9527 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -8,9 +8,9 @@ process RMARKDOWNNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : - 'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index fabb3234fdd..d9e1947e05c 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -3,9 +3,9 @@ process ROARY { label 'process_medium' conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' : - 'quay.io/biocontainers/roary:3.13.0--pl526h516909a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/roary:3.13.0--pl526h516909a_0" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 1ab3a63570e..0f466078c33 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -3,9 +3,9 @@ process RSEM_CALCULATEEXPRESSION { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : - 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index da11be451aa..f286a172ef2 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -3,9 +3,9 @@ process RSEM_PREPAREREFERENCE { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : - 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } input: path fasta, stageAs: "rsem/*" diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index 958221fdeed..c6620b7ed8b 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -3,9 +3,9 @@ process RSEQC_BAMSTAT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index 23c1b688274..ee130c73b47 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -3,9 +3,9 @@ process RSEQC_INFEREXPERIMENT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index b05661de175..e2a703375ff 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -3,9 +3,9 @@ process RSEQC_INNERDISTANCE { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index c3401dc51a5..c21a48c3ae5 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -3,9 +3,9 @@ process RSEQC_JUNCTIONANNOTATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 11b629040bc..cacd49d154e 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -3,9 +3,9 @@ process RSEQC_JUNCTIONSATURATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index 3198c5c6660..2174342505b 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -3,9 +3,9 @@ process RSEQC_READDISTRIBUTION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index cb989a5f202..7885bd94ec1 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -3,9 +3,9 @@ process RSEQC_READDUPLICATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 67493371b79..dd04384675b 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -3,9 +3,9 @@ process RSEQC_TIN { label 'process_high' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 9045b5b871c..6e5d2a81c3f 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -3,9 +3,9 @@ process RTGTOOLS_PEDFILTER { label 'process_low' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - 'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 27a488f70f4..2f05283b7d6 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -3,9 +3,9 @@ process RTGTOOLS_VCFEVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - 'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 737087f968e..3f76ddec490 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -3,9 +3,9 @@ process SALMON_INDEX { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : - 'quay.io/biocontainers/salmon:1.5.2--h84f40af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } input: path genome_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index bd4792c52e6..8ed4acdee0b 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -3,9 +3,9 @@ process SALMON_QUANT { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : - 'quay.io/biocontainers/salmon:1.5.2--h84f40af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 225c715280a..0d0f8b20f7f 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -3,9 +3,9 @@ process SAMBLASTER { label 'process_low' conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' : - 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 3a3bb8522be..dd00705f44e 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_AMPLICONCLIP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index 9301d1d33c8..bb67229f7bd 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_BAM2FQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 4944b70afe0..a9fdff834d3 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_COLLATE { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 3d9becdae4f..00fb07f92b0 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_COLLATEFASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index eea00179c66..eb5ee60f59f 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index d5f2ba60c9b..eb114e57a49 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_DEPTH { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 91f782b13f8..4b46a2f27ad 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_DICT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index ef940db2792..45e3943cb42 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_FAIDX { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 130c2a5a9f4..22508240a82 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_FASTA { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 8d9b9d0843f..fc6798598f9 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_FASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index f5e16f67dcb..bd31c741b76 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_FIXMATE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index c3152acaef4..2024239c1a5 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_FLAGSTAT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 54c36f039de..fe6adb87c82 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_GETRG { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 87618e5f38b..8fdee9f041c 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_IDXSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e04e63e8591..c3dd5fe3bcd 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 0c7a1598426..80976147f96 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_MARKDUP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 91f141166cf..03df854a89a 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index fe8e32b4cec..115e7a224e0 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_MPILEUP { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index ab7f1ccaf02..5cfe8fbb821 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 9b0c3867899..28f6de03b92 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index b2f5c678047..c1c6f4457f2 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -3,9 +3,9 @@ process SAMTOOLS_VIEW { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index cfa58ab23e5..115e577fecf 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -3,9 +3,9 @@ process SCOARY { label 'process_low' conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' : - 'quay.io/biocontainers/scoary:1.6.16--py_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/scoary:1.6.16--py_2" } input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index cceceb052c2..18bf627c196 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -3,9 +3,9 @@ process SCRAMBLE_CLUSTERANALYSIS { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': - 'quay.io/biocontainers/scramble:1.0.1--h779adbc_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } input: tuple val(meta), path(clusters) diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 1a90396ed67..de6cedf008e 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -3,9 +3,9 @@ process SCRAMBLE_CLUSTERIDENTIFIER { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': - 'quay.io/biocontainers/scramble:1.0.1--h779adbc_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index f0311f2fa13..2a57a4a35a1 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -4,9 +4,9 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' : - 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" } input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 228b98bd791..126d520c46a 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -3,9 +3,9 @@ process SEQKIT_PAIR { label 'process_medium' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': - 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index db189ef6f21..b20eb1d64c9 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -3,9 +3,9 @@ process SEQKIT_REPLACE { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': - 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index ff91d86bd95..d66ce529a09 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -3,9 +3,9 @@ process SEQKIT_SPLIT2 { label 'process_medium' conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : - 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index 28ac77b71db..f11461498d8 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -3,9 +3,9 @@ process SEQKIT_STATS { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0': - 'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.2.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index a5393cf63b3..ee1083ce961 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -3,9 +3,9 @@ process SEQSERO2 { label 'process_low' conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : - 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqsero2:1.2.1--py_0" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 9c98ed2cba3..04368f8ac84 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -3,9 +3,9 @@ process SEQTK_MERGEPE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index 75ed41ecc03..44b58d3923a 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -3,9 +3,9 @@ process SEQTK_RENAME { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index 1161993e6ca..c3882b2c0d9 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -3,9 +3,9 @@ process SEQTK_SAMPLE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 42cc6a8763a..4b78d45c2b7 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -3,9 +3,9 @@ process SEQTK_SEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 8a9a5b8d50c..4a2270bcff9 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -3,9 +3,9 @@ process SEQTK_SUBSEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: path sequences diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index f150e0bd167..8d1b52fc602 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -3,9 +3,9 @@ process SEQUENZAUTILS_BAM2SEQZ { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : - 'quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } input: tuple val(meta), path(normalbam), path(tumourbam) diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 23cc75b6f70..6cd8062aeb8 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -3,9 +3,9 @@ process SEQUENZAUTILS_GCWIGGLE { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : - 'quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 405bfd33bb1..137bd8f935b 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -4,9 +4,9 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' : - 'quay.io/biocontainers/seqwish:0.7.6--h5b5514e_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seqwish:0.7.6--h5b5514e_1" } input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 2179eb47a97..68bad5959af 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -3,9 +3,9 @@ process SEROBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1': - 'quay.io/biocontainers/seroba:1.0.2--pyhdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/seroba:1.0.2--pyhdfd78af_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index d22322a26fe..450b7bd64da 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -3,9 +3,9 @@ process SEXDETERRMINE { label 'process_single' conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1': - 'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sexdeterrmine:1.1.2--hdfd78af_1" } input: tuple val(meta), path(depth) diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 3bdb0bf9154..9ae4f4c6543 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -3,9 +3,9 @@ process SHASTA { label 'process_medium' conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shasta:0.8.0--h7d875b9_0': - 'quay.io/biocontainers/shasta:0.8.0--h7d875b9_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/shasta:0.8.0--h7d875b9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index 0e288435ad1..5fcae1a8f69 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -3,7 +3,7 @@ process SHASUM { label 'process_low' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index 9d5c189a400..1c3916d9d5b 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -3,9 +3,9 @@ process SHIGATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0': - 'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/shigatyper:2.0.1--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 20a4548fa8c..6c92bbab0b5 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -3,9 +3,9 @@ process SHOVILL { label 'process_medium' conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' : - 'quay.io/biocontainers/shovill:1.1.0--0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/shovill:1.1.0--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 0301d0531ca..ae318feaa8f 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -3,9 +3,9 @@ process SISTR { label 'process_medium' conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2': - 'quay.io/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sistr_cmd:1.1.1--pyh864c0ab_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 04abd27002e..d0fc23653bf 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -4,9 +4,9 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2': - 'quay.io/biocontainers/slimfastq:2.04--h87f3376_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/slimfastq:2.04--h87f3376_2" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index 96a2159b994..423d880263a 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -3,9 +3,9 @@ process SNAPALIGNER_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': - 'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index d084d8414e8..e8f8d482165 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -3,9 +3,9 @@ process SNAPALIGNER_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': - 'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } input: path fasta diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index c6e95c5b12e..895d230050b 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -3,9 +3,9 @@ process SNIPPY_CORE { label 'process_medium' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2': - 'quay.io/biocontainers/snippy:4.6.0--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_1" } input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index 5ecdbea88cb..dbeb629dea5 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -3,9 +3,9 @@ process SNIPPY_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' : - 'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 29febc6851a..1b673d7a7b7 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -3,9 +3,9 @@ process SNPDISTS { label 'process_low' conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0' : - 'quay.io/biocontainers/snp-dists:0.8.2--h5bf99c6_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snp-dists:0.8.2--h5bf99c6_0" } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index ac615bf73e2..4397aafc5fb 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -3,9 +3,9 @@ process SNPEFF { label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : - 'quay.io/biocontainers/snpeff:5.1--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snpeff:5.1--hdfd78af_2" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index 8531b4cb7b9..3c7eb901550 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -3,9 +3,9 @@ process SNPSIFT_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : - 'quay.io/biocontainers/snpsift:4.3.1t--hdfd78af_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snpsift:4.3.1t--hdfd78af_3" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index 33b1a2c9456..aaf56400b57 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -2,9 +2,9 @@ process SNPSITES { label 'process_medium' conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' : - 'quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/snp-sites:2.5.1--hed695b0_0" } input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 99b42d77ba8..05f285a80ad 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -4,9 +4,9 @@ process SOMALIER_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - 'quay.io/biocontainers/somalier:0.2.15--h37c5b7d_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index dfe91262e23..890c8fc516b 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -4,9 +4,9 @@ process SOMALIER_RELATE { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - 'quay.io/biocontainers/somalier:0.2.15--h37c5b7d_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } input: tuple val(meta), path(extract) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 419d2914950..31e299c76a6 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,9 +3,9 @@ process SORTMERNA { label "process_high" conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' : - 'quay.io/biocontainers/sortmerna:4.3.4--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sortmerna:4.3.4--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index e16b605fec7..1afc834817f 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -3,9 +3,9 @@ process SOURMASH_SKETCH { label 'process_low' conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0': - 'quay.io/biocontainers/sourmash:4.2.4--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sourmash:4.2.4--hdfd78af_0" } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index a467fcd729d..2c1cd19c8f9 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -3,9 +3,9 @@ process SPADES { label 'process_high' conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' : - 'quay.io/biocontainers/spades:3.15.4--h95f258a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/spades:3.15.4--h95f258a_0" } input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index 2a116f093c5..463ddf2ec4c 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -3,9 +3,9 @@ process SPATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' : - 'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/spatyper:0.3.3--pyhdfd78af_3" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index 18f46e51777..539e52777bd 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -3,9 +3,9 @@ process SRATOOLS_FASTERQDUMP { label 'process_medium' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : - 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" } input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 3426ae1262a..dbf25e77f16 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -3,9 +3,9 @@ process SRATOOLS_PREFETCH { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : - 'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } input: tuple val(meta), val(id) diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index e8a91716af1..c34102c88e4 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -3,9 +3,9 @@ process SRST2_SRST2 { label 'process_low' conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2': - 'quay.io/biocontainers/srst2:0.2.0--py27_2'}" + "${params.docker_url ?: 'quay.io/biocontainers'}/srst2:0.2.0--py27_2"} input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 4e169878c1d..348fba4d9a8 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -4,9 +4,9 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0': - 'quay.io/biocontainers/ssuissero:1.0.1--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ssuissero:1.0.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index e24fb2cb166..b707675b953 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -3,9 +3,9 @@ process STADENIOLIB_SCRAMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' : - 'quay.io/biocontainers/staden_io_lib:1.14.14--h0d9da7e_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/staden_io_lib:1.14.14--h0d9da7e_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index dd173c2fb7e..82b76972f3e 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -3,9 +3,9 @@ process STAPHOPIASCCMEC { label 'process_low' conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' : - 'quay.io/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/staphopia-sccmec:1.0.0--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 47c58eb0b75..365d6da2d32 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,9 +3,9 @@ process STAR_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : - 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 6ec634a17a3..b4551be3bea 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,9 +3,9 @@ process STAR_GENOMEGENERATE { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : - 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } input: path fasta diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index ddfa0070d6a..de4e3dbe150 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -3,9 +3,9 @@ process STRANGER { label 'process_low' conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0': - 'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/stranger:0.8.1--pyh5e36f6f_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 1f59bee157a..d47b9f15df8 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -3,9 +3,9 @@ process STRELKA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : - 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 08b298a4631..7ca59636205 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -3,9 +3,9 @@ process STRELKA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : - 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 4cdaafe202a..cf9e193e7b8 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -3,9 +3,9 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index b403edee6aa..2a70a04e909 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -3,9 +3,9 @@ process STRINGTIE_STRINGTIE { label 'process_medium' conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 18e2a92bb05..20d2ec8c841 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -3,9 +3,9 @@ process SUBREAD_FEATURECOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - 'quay.io/biocontainers/subread:2.0.1--hed695b0_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/subread:2.0.1--hed695b0_0" } input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 477dbb0d31d..e19ee1fa13b 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -2,9 +2,9 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0': - 'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" } input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index dbab5259c30..6200338ce01 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -3,9 +3,9 @@ process SVDB_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': - 'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/svdb:2.6.1--py39h5371cbf_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index 104afc202dc..e2e95049db7 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -3,9 +3,9 @@ process SVTK_STANDARDIZE { label 'process_low' conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2': - 'quay.io/biocontainers/svtk:0.0.20190615--py37h73a75cf_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/svtk:0.0.20190615--py37h73a75cf_2" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index aaef7859439..70fbf2165e6 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -3,9 +3,9 @@ process TABIX_BGZIP { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 0d05984add7..bdd6ab6db72 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -3,9 +3,9 @@ process TABIX_BGZIPTABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 21b2e79f484..e91a8a6d937 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -3,9 +3,9 @@ process TABIX_TABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 445fa1be14b..09ce7c1d7b8 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -3,9 +3,9 @@ process TAILFINDR { label 'process_high' conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0': - 'quay.io/biocontainers/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" } input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index 17c94a34bdb..f118308e40f 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -3,9 +3,9 @@ process TBPROFILER_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' : - 'quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/tb-profiler:3.0.8--pypyh5e36f6f_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 4d7e28271f9..3efd0107872 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -3,9 +3,9 @@ process TIDDIT_COV { label 'process_low' conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' : - 'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/tiddit:3.0.0--py39h59fae87_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 2e876ef1ae3..6d7b0f01202 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -3,9 +3,9 @@ process TIDDIT_SV { label 'process_medium' conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' : - 'quay.io/biocontainers/tiddit:3.1.0--py39h59fae87_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/tiddit:3.1.0--py39h59fae87_1" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index 9d5c20f2062..6d12391748c 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -3,7 +3,7 @@ process TRANSDECODER_LONGORF { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4' : 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index dccc031ce16..b647c1180a0 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -3,7 +3,7 @@ process TRANSDECODER_PREDICT { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4': 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 5b45e4d7f7c..cf96c35b54e 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -3,9 +3,9 @@ process TRIMGALORE { label 'process_high' conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/trim-galore:0.6.7--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 216fa06f66d..55b3f23373b 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -3,9 +3,9 @@ process TRIMMOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2': - 'quay.io/biocontainers/trimmomatic:0.39--hdfd78af_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/trimmomatic:0.39--hdfd78af_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index 42dd08bb1b5..86519b6aca3 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -4,9 +4,9 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' : - 'quay.io/biocontainers/ucsc-bedclip:377--h0b8a92a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bedclip:377--h0b8a92a_2" } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index a2979e04455..14ab6a813f8 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -4,9 +4,9 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' : - 'quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bedgraphtobigwig:377--h446ed27_1" } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index 3acc8f3645f..8ea62b4af02 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -4,9 +4,9 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--ha8a8165_3' : - 'quay.io/biocontainers/ucsc-bedtobigbed:377--ha8a8165_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bedtobigbed:377--ha8a8165_3" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index 05e14278848..676fcde8477 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -4,9 +4,9 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' : - 'quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index 1dc96975a3d..082469a6366 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -4,9 +4,9 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' : - 'quay.io/biocontainers/ucsc-liftover:377--h0b8a92a_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-liftover:377--h0b8a92a_3" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index cf76cf0a657..73603f90e64 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -4,9 +4,9 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' : - 'quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-wigtobigwig:377--h0b8a92a_2" } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index a6cb6dcf146..f5e32f54610 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -3,9 +3,9 @@ process ULTRA_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0': - 'quay.io/biocontainers/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 731a74a9100..abf40c565bf 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -3,9 +3,9 @@ process ULTRA_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0': - 'quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } input: path fasta diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index c86a5802238..efb78371d7b 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -3,9 +3,9 @@ process ULTRA_PIPELINE { label 'process_high' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' : - 'quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 48559d818bc..36669cbc310 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -3,9 +3,9 @@ process UMITOOLS_DEDUP { label "process_medium" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : - 'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 22a405b9704..f8a3e3c8c71 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -3,9 +3,9 @@ process UMITOOLS_EXTRACT { label "process_low" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : - 'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index 4d3721b0367..3d42fca8ef5 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -3,9 +3,9 @@ process UNICYCLER { label 'process_high' conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : - 'quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/unicycler:0.4.8--py38h8162308_3" } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 71eea7b2c68..df5821cdeb1 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -3,7 +3,7 @@ process UNTAR { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index bb645ca63f0..230a6469971 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -3,9 +3,9 @@ process UNZIP { label 'process_single' conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' : - 'quay.io/biocontainers/p7zip:15.09--h2d50403_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/p7zip:15.09--h2d50403_4" } input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 42c9b5136a1..b72eda3df1f 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -3,9 +3,9 @@ process VARDICTJAVA { label 'process_medium' conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': - 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vardict-java:1.8.3--hdfd78af_0" } input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 8f08077861e..5a86083bc74 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -4,9 +4,9 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' : - 'quay.io/biocontainers/variantbam:1.4.4a--h7d7f7ad_5' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/variantbam:1.4.4a--h7d7f7ad_5" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index a8d52fc60d2..617ce8cd08f 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,9 +4,9 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1': - 'quay.io/biocontainers/vcf2db:2020.02.24--hdfd78af_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vcf2db:2020.02.24--hdfd78af_1" } input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 52a59149e43..3c15533a3cc 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -5,9 +5,9 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0': - 'quay.io/biocontainers/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" } input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 6f264af2dc6..7cb1b6e5c23 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -3,9 +3,9 @@ process VCFANNO { label 'process_low' conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': - 'quay.io/biocontainers/vcfanno:0.3.3--h9ee0642_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vcfanno:0.3.3--h9ee0642_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 0eb9cd7bda2..dd7fab79b15 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -3,9 +3,9 @@ process VCFLIB_VCFBREAKMULTI { label 'process_low' conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - 'quay.io/biocontainers/vcflib:1.0.3--ha025227_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vcflib:1.0.3--ha025227_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index 707f074b841..e8ff0b1afe9 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -4,9 +4,9 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - 'quay.io/biocontainers/vcflib:1.0.3--hecb563c_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vcflib:1.0.3--hecb563c_1" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index feefb0e3f8d..eff434128e0 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -3,9 +3,9 @@ process VCFTOOLS { label 'process_single' conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : - 'quay.io/biocontainers/vcftools:0.1.16--he513fc3_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vcftools:0.1.16--he513fc3_4" } input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index cada11f22f9..226b79d1367 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,9 +3,9 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : - 'quay.io/biocontainers/verifybamid2:2.0.1--h19d48f6_8' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/verifybamid2:2.0.1--h19d48f6_8" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index e2ffbe8357a..44aefc3cf4f 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -3,9 +3,9 @@ process VSEARCH_SINTAX { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - 'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index c85546c1fb6..8b432a0b534 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -3,9 +3,9 @@ process VSEARCH_USEARCHGLOBAL { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - 'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index bca784db6a6..63d01ff4889 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -3,9 +3,9 @@ process WGSIM { label 'process_medium' conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/wgsim:1.0--h5bf99c6_4': - 'quay.io/biocontainers/wgsim:1.0--h5bf99c6_4' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/wgsim:1.0--h5bf99c6_4" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index b6f39adb16a..18eeec34eba 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -3,9 +3,9 @@ process WHAMG { label 'process_medium' conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1': - 'quay.io/biocontainers/wham:1.8.0.1.2017.05.03--h8b12597_1' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/wham:1.8.0.1.2017.05.03--h8b12597_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index b6bae9a941e..b8cbddec1d3 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -3,9 +3,9 @@ process YARA_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' : - 'quay.io/biocontainers/yara:1.0.2--2' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/yara:1.0.2--2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index c2624ab304e..038c04e7b70 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -3,9 +3,9 @@ process YARA_MAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : - 'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' }" + "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" } input: tuple val(meta), path(reads) diff --git a/tests/modules/nf-core/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config index 0903de1baa7..0a9ffca7f5f 100644 --- a/tests/modules/nf-core/vcf2maf/nextflow.config +++ b/tests/modules/nf-core/vcf2maf/nextflow.config @@ -6,7 +6,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: 'test_vcf2maf_no_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" - container = "quay.io/biocontainers/vcf2maf:1.6.21--hdfd78af_0" + container = ${params.docker_url ?: 'quay.io/biocontainers'}/vcf2maf:1.6.21--hdfd78af_0 } withName: 'test_vcf2maf_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species}" From c709e73d7f6876b205ecb84968b17ff6c1893e18 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 12:35:25 +0200 Subject: [PATCH 07/21] style: docker_url => docker_registry --- modules/nf-core/abacas/main.nf | 2 +- modules/nf-core/abricate/run/main.nf | 2 +- modules/nf-core/abricate/summary/main.nf | 2 +- modules/nf-core/adapterremoval/main.nf | 2 +- modules/nf-core/adapterremovalfixprefix/main.nf | 2 +- modules/nf-core/agrvate/main.nf | 2 +- modules/nf-core/allelecounter/main.nf | 2 +- modules/nf-core/ampir/main.nf | 2 +- modules/nf-core/amplify/predict/main.nf | 2 +- modules/nf-core/amps/main.nf | 2 +- modules/nf-core/amrfinderplus/run/main.nf | 2 +- modules/nf-core/amrfinderplus/update/main.nf | 2 +- modules/nf-core/angsd/docounts/main.nf | 2 +- modules/nf-core/antismash/antismashlite/main.nf | 2 +- .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 2 +- modules/nf-core/aria2/main.nf | 2 +- modules/nf-core/ariba/getref/main.nf | 2 +- modules/nf-core/ariba/run/main.nf | 2 +- modules/nf-core/arriba/main.nf | 2 +- modules/nf-core/artic/guppyplex/main.nf | 2 +- modules/nf-core/artic/minion/main.nf | 2 +- modules/nf-core/ascat/main.nf | 2 +- modules/nf-core/assemblyscan/main.nf | 2 +- modules/nf-core/ataqv/ataqv/main.nf | 2 +- modules/nf-core/ataqv/mkarv/main.nf | 2 +- modules/nf-core/atlas/call/main.nf | 2 +- modules/nf-core/atlas/pmd/main.nf | 2 +- modules/nf-core/atlas/recal/main.nf | 2 +- modules/nf-core/atlas/splitmerge/main.nf | 2 +- modules/nf-core/bakta/main.nf | 2 +- modules/nf-core/bamaligncleaner/main.nf | 2 +- modules/nf-core/bamcmp/main.nf | 2 +- modules/nf-core/bamtools/convert/main.nf | 2 +- modules/nf-core/bamtools/split/main.nf | 2 +- 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| 2 +- modules/nf-core/expansionhunter/main.nf | 2 +- modules/nf-core/faqcs/main.nf | 2 +- modules/nf-core/fargene/main.nf | 2 +- modules/nf-core/fastani/main.nf | 2 +- modules/nf-core/fastawindows/main.nf | 2 +- modules/nf-core/fastp/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/fastqscan/main.nf | 2 +- modules/nf-core/fasttree/main.nf | 2 +- modules/nf-core/ffq/main.nf | 2 +- modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 2 +- modules/nf-core/fgbio/fastqtobam/main.nf | 2 +- modules/nf-core/fgbio/groupreadsbyumi/main.nf | 2 +- modules/nf-core/fgbio/sortbam/main.nf | 2 +- modules/nf-core/fgbio/zipperbams/main.nf | 2 +- modules/nf-core/filtlong/main.nf | 2 +- modules/nf-core/flash/main.nf | 2 +- modules/nf-core/flye/main.nf | 2 +- modules/nf-core/fq/lint/main.nf | 2 +- modules/nf-core/freebayes/main.nf | 2 +- modules/nf-core/gamma/gamma/main.nf | 2 +- modules/nf-core/gappa/examineassign/main.nf | 2 +- modules/nf-core/gappa/examinegraft/main.nf | 2 +- 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modules/nf-core/lissero/main.nf | 2 +- modules/nf-core/lofreq/call/main.nf | 2 +- modules/nf-core/lofreq/callparallel/main.nf | 2 +- modules/nf-core/lofreq/filter/main.nf | 2 +- modules/nf-core/lofreq/indelqual/main.nf | 2 +- modules/nf-core/macrel/contigs/main.nf | 2 +- modules/nf-core/macs2/callpeak/main.nf | 2 +- modules/nf-core/mafft/main.nf | 2 +- modules/nf-core/malt/build/main.nf | 2 +- modules/nf-core/malt/run/main.nf | 2 +- modules/nf-core/maltextract/main.nf | 2 +- modules/nf-core/manta/convertinversion/main.nf | 2 +- modules/nf-core/manta/germline/main.nf | 2 +- modules/nf-core/manta/somatic/main.nf | 2 +- modules/nf-core/manta/tumoronly/main.nf | 2 +- modules/nf-core/mapdamage2/main.nf | 2 +- modules/nf-core/mash/dist/main.nf | 2 +- modules/nf-core/mash/screen/main.nf | 2 +- modules/nf-core/mash/sketch/main.nf | 2 +- modules/nf-core/mashtree/main.nf | 2 +- modules/nf-core/maxbin2/main.nf | 2 +- modules/nf-core/maxquant/lfq/main.nf | 2 +- modules/nf-core/mcroni/main.nf | 2 +- modules/nf-core/medaka/main.nf | 2 +- modules/nf-core/megahit/main.nf | 2 +- modules/nf-core/megan/daa2info/main.nf | 2 +- modules/nf-core/megan/rma2info/main.nf | 2 +- modules/nf-core/meningotype/main.nf | 2 +- modules/nf-core/merqury/main.nf | 2 +- modules/nf-core/meryl/count/main.nf | 2 +- modules/nf-core/meryl/histogram/main.nf | 2 +- modules/nf-core/meryl/unionsum/main.nf | 2 +- modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf | 2 +- modules/nf-core/metabat2/metabat2/main.nf | 2 +- modules/nf-core/metaphlan3/mergemetaphlantables/main.nf | 2 +- modules/nf-core/metaphlan3/metaphlan3/main.nf | 2 +- modules/nf-core/methyldackel/extract/main.nf | 2 +- modules/nf-core/methyldackel/mbias/main.nf | 2 +- modules/nf-core/minia/main.nf | 2 +- modules/nf-core/miniasm/main.nf | 2 +- modules/nf-core/minimap2/align/main.nf | 2 +- modules/nf-core/minimap2/index/main.nf | 2 +- modules/nf-core/mlst/main.nf | 2 +- modules/nf-core/mobsuite/recon/main.nf | 2 +- modules/nf-core/mosdepth/main.nf | 2 +- modules/nf-core/motus/downloaddb/main.nf | 2 +- modules/nf-core/motus/merge/main.nf | 2 +- modules/nf-core/motus/profile/main.nf | 2 +- modules/nf-core/msisensor/msi/main.nf | 2 +- modules/nf-core/msisensor/scan/main.nf | 2 +- modules/nf-core/msisensor2/msi/main.nf | 2 +- modules/nf-core/msisensor2/scan/main.nf | 2 +- modules/nf-core/msisensorpro/msi_somatic/main.nf | 2 +- modules/nf-core/msisensorpro/scan/main.nf | 2 +- modules/nf-core/mtnucratio/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 2 +- modules/nf-core/multivcfanalyzer/main.nf | 2 +- modules/nf-core/mummer/main.nf | 2 +- modules/nf-core/muscle/main.nf | 2 +- modules/nf-core/mykrobe/predict/main.nf | 2 +- modules/nf-core/nanolyse/main.nf | 2 +- modules/nf-core/nanoplot/main.nf | 2 +- modules/nf-core/ncbigenomedownload/main.nf | 2 +- modules/nf-core/nextclade/datasetget/main.nf | 2 +- modules/nf-core/nextclade/run/main.nf | 2 +- modules/nf-core/nextgenmap/main.nf | 2 +- modules/nf-core/ngmaster/main.nf | 2 +- modules/nf-core/ngscheckmate/ncm/main.nf | 2 +- modules/nf-core/nucmer/main.nf | 2 +- modules/nf-core/optitype/main.nf | 2 +- modules/nf-core/pairix/main.nf | 2 +- modules/nf-core/pairtools/dedup/main.nf | 2 +- modules/nf-core/pairtools/flip/main.nf | 2 +- modules/nf-core/pairtools/parse/main.nf | 2 +- modules/nf-core/pairtools/restrict/main.nf | 2 +- modules/nf-core/pairtools/select/main.nf | 2 +- modules/nf-core/pairtools/sort/main.nf | 2 +- modules/nf-core/panaroo/run/main.nf | 2 +- modules/nf-core/pangolin/main.nf | 2 +- modules/nf-core/paraclu/main.nf | 2 +- modules/nf-core/pasty/main.nf | 2 +- modules/nf-core/pbbam/pbmerge/main.nf | 2 +- modules/nf-core/pbccs/main.nf | 2 +- modules/nf-core/pbptyper/main.nf | 2 +- modules/nf-core/pear/main.nf | 2 +- modules/nf-core/peddy/main.nf | 2 +- modules/nf-core/phantompeakqualtools/main.nf | 2 +- modules/nf-core/phyloflash/main.nf | 2 +- modules/nf-core/picard/addorreplacereadgroups/main.nf | 2 +- modules/nf-core/picard/cleansam/main.nf | 2 +- modules/nf-core/picard/collecthsmetrics/main.nf | 2 +- modules/nf-core/picard/collectmultiplemetrics/main.nf | 2 +- modules/nf-core/picard/collectwgsmetrics/main.nf | 2 +- modules/nf-core/picard/createsequencedictionary/main.nf | 2 +- modules/nf-core/picard/crosscheckfingerprints/main.nf | 2 +- modules/nf-core/picard/fastqtosam/main.nf | 2 +- modules/nf-core/picard/filtersamreads/main.nf | 2 +- modules/nf-core/picard/fixmateinformation/main.nf | 2 +- modules/nf-core/picard/liftovervcf/main.nf | 2 +- modules/nf-core/picard/markduplicates/main.nf | 2 +- modules/nf-core/picard/mergesamfiles/main.nf | 2 +- modules/nf-core/picard/renamesampleinvcf/main.nf | 2 +- modules/nf-core/picard/sortsam/main.nf | 2 +- modules/nf-core/picard/sortvcf/main.nf | 2 +- modules/nf-core/pints/caller/main.nf | 2 +- modules/nf-core/pirate/main.nf | 2 +- modules/nf-core/plasmidfinder/main.nf | 2 +- modules/nf-core/plasmidid/main.nf | 2 +- modules/nf-core/plink/extract/main.nf | 2 +- modules/nf-core/plink/vcf/main.nf | 2 +- modules/nf-core/plink2/extract/main.nf | 2 +- modules/nf-core/plink2/score/main.nf | 2 +- modules/nf-core/plink2/vcf/main.nf | 2 +- modules/nf-core/pmdtools/filter/main.nf | 2 +- modules/nf-core/porechop/main.nf | 2 +- modules/nf-core/preseq/ccurve/main.nf | 2 +- modules/nf-core/preseq/lcextrap/main.nf | 2 +- modules/nf-core/prinseqplusplus/main.nf | 2 +- modules/nf-core/prodigal/main.nf | 2 +- modules/nf-core/prokka/main.nf | 2 +- modules/nf-core/pycoqc/main.nf | 2 +- modules/nf-core/pydamage/analyze/main.nf | 2 +- modules/nf-core/pydamage/filter/main.nf | 2 +- modules/nf-core/qcat/main.nf | 2 +- modules/nf-core/qualimap/bamqc/main.nf | 2 +- modules/nf-core/qualimap/bamqccram/main.nf | 2 +- modules/nf-core/qualimap/rnaseq/main.nf | 2 +- modules/nf-core/quast/main.nf | 2 +- modules/nf-core/racon/main.nf | 2 +- modules/nf-core/rapidnj/main.nf | 2 +- modules/nf-core/rasusa/main.nf | 2 +- modules/nf-core/raven/main.nf | 2 +- modules/nf-core/raxmlng/main.nf | 2 +- modules/nf-core/rgi/main/main.nf | 2 +- modules/nf-core/rhocall/annotate/main.nf | 2 +- modules/nf-core/rmarkdownnotebook/main.nf | 2 +- modules/nf-core/roary/main.nf | 2 +- modules/nf-core/rsem/calculateexpression/main.nf | 2 +- modules/nf-core/rsem/preparereference/main.nf | 2 +- modules/nf-core/rseqc/bamstat/main.nf | 2 +- modules/nf-core/rseqc/inferexperiment/main.nf | 2 +- modules/nf-core/rseqc/innerdistance/main.nf | 2 +- modules/nf-core/rseqc/junctionannotation/main.nf | 2 +- modules/nf-core/rseqc/junctionsaturation/main.nf | 2 +- modules/nf-core/rseqc/readdistribution/main.nf | 2 +- modules/nf-core/rseqc/readduplication/main.nf | 2 +- modules/nf-core/rseqc/tin/main.nf | 2 +- modules/nf-core/rtgtools/pedfilter/main.nf | 2 +- modules/nf-core/rtgtools/vcfeval/main.nf | 2 +- modules/nf-core/salmon/index/main.nf | 2 +- modules/nf-core/salmon/quant/main.nf | 2 +- modules/nf-core/samblaster/main.nf | 2 +- modules/nf-core/samtools/ampliconclip/main.nf | 2 +- modules/nf-core/samtools/bam2fq/main.nf | 2 +- modules/nf-core/samtools/collate/main.nf | 2 +- modules/nf-core/samtools/collatefastq/main.nf | 2 +- modules/nf-core/samtools/convert/main.nf | 2 +- modules/nf-core/samtools/depth/main.nf | 2 +- modules/nf-core/samtools/dict/main.nf | 2 +- modules/nf-core/samtools/faidx/main.nf | 2 +- modules/nf-core/samtools/fasta/main.nf | 2 +- modules/nf-core/samtools/fastq/main.nf | 2 +- modules/nf-core/samtools/fixmate/main.nf | 2 +- modules/nf-core/samtools/flagstat/main.nf | 2 +- modules/nf-core/samtools/getrg/main.nf | 2 +- modules/nf-core/samtools/idxstats/main.nf | 2 +- modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/markdup/main.nf | 2 +- modules/nf-core/samtools/merge/main.nf | 2 +- modules/nf-core/samtools/mpileup/main.nf | 2 +- modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/scoary/main.nf | 2 +- modules/nf-core/scramble/clusteranalysis/main.nf | 2 +- modules/nf-core/scramble/clusteridentifier/main.nf | 2 +- modules/nf-core/seacr/callpeak/main.nf | 2 +- modules/nf-core/seqkit/pair/main.nf | 2 +- modules/nf-core/seqkit/replace/main.nf | 2 +- modules/nf-core/seqkit/split2/main.nf | 2 +- modules/nf-core/seqkit/stats/main.nf | 2 +- modules/nf-core/seqsero2/main.nf | 2 +- modules/nf-core/seqtk/mergepe/main.nf | 2 +- modules/nf-core/seqtk/rename/main.nf | 2 +- modules/nf-core/seqtk/sample/main.nf | 2 +- modules/nf-core/seqtk/seq/main.nf | 2 +- modules/nf-core/seqtk/subseq/main.nf | 2 +- modules/nf-core/sequenzautils/bam2seqz/main.nf | 2 +- modules/nf-core/sequenzautils/gcwiggle/main.nf | 2 +- modules/nf-core/seqwish/induce/main.nf | 2 +- modules/nf-core/seroba/run/main.nf | 2 +- modules/nf-core/sexdeterrmine/main.nf | 2 +- modules/nf-core/shasta/main.nf | 2 +- modules/nf-core/shigatyper/main.nf | 2 +- modules/nf-core/shovill/main.nf | 2 +- modules/nf-core/sistr/main.nf | 2 +- modules/nf-core/slimfastq/main.nf | 2 +- modules/nf-core/snapaligner/align/main.nf | 2 +- modules/nf-core/snapaligner/index/main.nf | 2 +- modules/nf-core/snippy/core/main.nf | 2 +- modules/nf-core/snippy/run/main.nf | 2 +- modules/nf-core/snpdists/main.nf | 2 +- modules/nf-core/snpeff/main.nf | 2 +- modules/nf-core/snpsift/split/main.nf | 2 +- modules/nf-core/snpsites/main.nf | 2 +- modules/nf-core/somalier/extract/main.nf | 2 +- modules/nf-core/somalier/relate/main.nf | 2 +- modules/nf-core/sortmerna/main.nf | 2 +- modules/nf-core/sourmash/sketch/main.nf | 2 +- modules/nf-core/spades/main.nf | 2 +- modules/nf-core/spatyper/main.nf | 2 +- modules/nf-core/sratools/fasterqdump/main.nf | 2 +- modules/nf-core/sratools/prefetch/main.nf | 2 +- modules/nf-core/srst2/srst2/main.nf | 2 +- modules/nf-core/ssuissero/main.nf | 2 +- modules/nf-core/stadeniolib/scramble/main.nf | 2 +- modules/nf-core/staphopiasccmec/main.nf | 2 +- modules/nf-core/star/align/main.nf | 2 +- modules/nf-core/star/genomegenerate/main.nf | 2 +- modules/nf-core/stranger/main.nf | 2 +- modules/nf-core/strelka/germline/main.nf | 2 +- modules/nf-core/strelka/somatic/main.nf | 2 +- modules/nf-core/stringtie/merge/main.nf | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 2 +- modules/nf-core/subread/featurecounts/main.nf | 2 +- modules/nf-core/svdb/merge/main.nf | 2 +- modules/nf-core/svdb/query/main.nf | 2 +- modules/nf-core/svtk/standardize/main.nf | 2 +- modules/nf-core/tabix/bgzip/main.nf | 2 +- modules/nf-core/tabix/bgziptabix/main.nf | 2 +- modules/nf-core/tabix/tabix/main.nf | 2 +- modules/nf-core/tailfindr/main.nf | 2 +- modules/nf-core/tbprofiler/profile/main.nf | 2 +- modules/nf-core/tiddit/cov/main.nf | 2 +- modules/nf-core/tiddit/sv/main.nf | 2 +- modules/nf-core/trimgalore/main.nf | 2 +- modules/nf-core/trimmomatic/main.nf | 2 +- modules/nf-core/ucsc/bedclip/main.nf | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 2 +- modules/nf-core/ucsc/bedtobigbed/main.nf | 2 +- modules/nf-core/ucsc/bigwigaverageoverbed/main.nf | 2 +- modules/nf-core/ucsc/liftover/main.nf | 2 +- modules/nf-core/ucsc/wigtobigwig/main.nf | 2 +- modules/nf-core/ultra/align/main.nf | 2 +- modules/nf-core/ultra/index/main.nf | 2 +- modules/nf-core/ultra/pipeline/main.nf | 2 +- modules/nf-core/umitools/dedup/main.nf | 2 +- modules/nf-core/umitools/extract/main.nf | 2 +- modules/nf-core/unicycler/main.nf | 2 +- modules/nf-core/unzip/main.nf | 2 +- modules/nf-core/vardictjava/main.nf | 2 +- modules/nf-core/variantbam/main.nf | 2 +- modules/nf-core/vcf2db/main.nf | 2 +- modules/nf-core/vcf2maf/main.nf | 2 +- modules/nf-core/vcfanno/main.nf | 2 +- modules/nf-core/vcflib/vcfbreakmulti/main.nf | 2 +- modules/nf-core/vcflib/vcfuniq/main.nf | 2 +- modules/nf-core/vcftools/main.nf | 2 +- modules/nf-core/verifybamid/verifybamid2/main.nf | 2 +- modules/nf-core/vsearch/sintax/main.nf | 2 +- modules/nf-core/vsearch/usearchglobal/main.nf | 2 +- modules/nf-core/wgsim/main.nf | 2 +- modules/nf-core/whamg/main.nf | 2 +- modules/nf-core/yara/index/main.nf | 2 +- modules/nf-core/yara/mapper/main.nf | 2 +- tests/config/nextflow.config | 2 +- tests/modules/nf-core/vcf2maf/nextflow.config | 2 +- 611 files changed, 611 insertions(+), 611 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index 389e8bc649a..3a90b7783bf 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -5,7 +5,7 @@ process ABACAS { conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/abacas:1.3.1--pl526_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/abacas:1.3.1--pl526_0" } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index c6a82be2dbc..843dc249b79 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -5,7 +5,7 @@ process ABRICATE_RUN { conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index 13281db950b..a6097ac313f 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -5,7 +5,7 @@ process ABRICATE_SUMMARY { conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 1a779751ca5..0427b9c4e6b 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -5,7 +5,7 @@ process ADAPTERREMOVAL { conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/adapterremoval:2.3.2--hb7ba0dd_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/adapterremoval:2.3.2--hb7ba0dd_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 595697c43df..45c444f6700 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -6,7 +6,7 @@ process ADAPTERREMOVALFIXPREFIX { conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/adapterremovalfixprefix:0.0.5--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/adapterremovalfixprefix:0.0.5--hdfd78af_2" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index c519b2a6f21..437eea38be0 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -5,7 +5,7 @@ process AGRVATE { conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/agrvate:1.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/agrvate:1.0.2--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index 3127d5608d9..0cc6d7735a0 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -5,7 +5,7 @@ process ALLELECOUNTER { conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cancerit-allelecount:4.3.0--h41abebc_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cancerit-allelecount:4.3.0--h41abebc_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index e4f2c0213cf..46da7276c94 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -5,7 +5,7 @@ process AMPIR { conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0': - "${params.docker_url ?: 'quay.io/biocontainers'}/r-ampir:1.1.0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ampir:1.1.0" } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 9eace6d397b..51fe2862403 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -6,7 +6,7 @@ process AMPLIFY_PREDICT { conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/amplify:1.0.3--py36hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/amplify:1.0.3--py36hdfd78af_0" } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 2f6592712e7..5d909a8cf54 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -4,7 +4,7 @@ process AMPS { conda (params.enable_conda ? "bioconda::hops=0.35" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 080b2b501b6..00730fc6277 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -5,7 +5,7 @@ process AMRFINDERPLUS_RUN { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 50ab02dbfdb..74a3e802249 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -5,7 +5,7 @@ process AMRFINDERPLUS_UPDATE { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index bbeeb24de3d..58b3e8a20ae 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -5,7 +5,7 @@ process ANGSD_DOCOUNTS { conda (params.enable_conda ? "bioconda::angsd=0.939" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/angsd:0.939--h468462d_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/angsd:0.939--h468462d_0" } input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 7bbfcfef4fb..28cf3ffedce 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -5,7 +5,7 @@ process ANTISMASH_ANTISMASHLITE { conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } containerOptions { workflow.containerEngine == 'singularity' ? diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 904243d3f27..2a3f27756cb 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -4,7 +4,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 4c55b561cd7..12167e00380 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -6,7 +6,7 @@ process ARIA2 { conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/aria2:1.36.0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/aria2:1.36.0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/aria2:1.36.0" } input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index 5f3f94d6dc4..abb0381bbd0 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -5,7 +5,7 @@ process ARIBA_GETREF { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': - "${params.docker_url ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 044cc8a93f2..4f8d07baba3 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -5,7 +5,7 @@ process ARIBA_RUN { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': - "${params.docker_url ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index c870717c174..11c781e2998 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -5,7 +5,7 @@ process ARRIBA { conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/arriba:2.3.0--haa8aa89_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/arriba:2.3.0--haa8aa89_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 81e3a081a54..98aca407f5b 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -5,7 +5,7 @@ process ARTIC_GUPPYPLEX { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index 39212c7061f..524aa79d968 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -5,7 +5,7 @@ process ARTIC_MINION { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index b5238880152..46728afcb0f 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -5,7 +5,7 @@ process ASCAT { conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" } input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 3fa07f860d7..edf271bd4f7 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -5,7 +5,7 @@ process ASSEMBLYSCAN { conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/assembly-scan:0.4.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/assembly-scan:0.4.1--pyhdfd78af_0" } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index 61d44602d1b..3f5864d72c3 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -5,7 +5,7 @@ process ATAQV_ATAQV { conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } input: tuple val(meta), path(bam), path(bai), path(peak_file) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 310461ddd87..75718b6ee74 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -4,7 +4,7 @@ process ATAQV_MKARV { conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index e33ddb5c22e..5ba4b080e89 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -5,7 +5,7 @@ process ATLAS_CALL { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index 3c3197b07ed..75bf97ce795 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -5,7 +5,7 @@ process ATLAS_PMD { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index 10368c9812e..2784b9f67c7 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -5,7 +5,7 @@ process ATLAS_RECAL { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index b47e3cf6aa1..25f13381002 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -5,7 +5,7 @@ process ATLAS_SPLITMERGE { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index 6c28af0bddf..b2be31f5749 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -5,7 +5,7 @@ process BAKTA { conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bakta:1.5.0--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bakta:1.5.0--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bakta:1.5.0--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index 70f9903afeb..ca0fb18b802 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -5,7 +5,7 @@ process BAMALIGNCLEANER { conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bamaligncleaner:0.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bamaligncleaner:0.2.1--pyhdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 49963eafe5f..26cdf5a385a 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -5,7 +5,7 @@ process BAMCMP { conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bamcmp:2.2--h05f6578_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bamcmp:2.2--h05f6578_0" } input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index d10136a4ebc..35bf0d2bf6f 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -5,7 +5,7 @@ process BAMTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index 70843cac54f..e5198942fee 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -5,7 +5,7 @@ process BAMTOOLS_SPLIT { conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bamtools:2.5.2--hd03093a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.2--hd03093a_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index edeb1a1514f..30fadd9cff4 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -5,7 +5,7 @@ process BAMTOOLS_STATS { conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index e02207abab4..1f7569b29d4 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -5,7 +5,7 @@ process BAMUTIL_TRIMBAM { conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bamutil:1.0.15--h2e03b76_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bamutil:1.0.15--h2e03b76_1" } input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 7a5f1789aeb..1292a833368 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -5,7 +5,7 @@ process BANDAGE_IMAGE { conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bandage:0.8.1--hc9558a2_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bandage:0.8.1--hc9558a2_2" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 07b20f31530..871108ff602 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -5,7 +5,7 @@ process BBMAP_ALIGN { conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 4ebe50f58d1..f571c95c1bb 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -5,7 +5,7 @@ process BBMAP_BBDUK { conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.90--he522d1c_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.90--he522d1c_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index ab8dda8dff3..86f77cceeda 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -4,7 +4,7 @@ process BBMAP_BBSPLIT { conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.93--he522d1c_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.93--he522d1c_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index e8758bf4df6..185e211442f 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -6,7 +6,7 @@ process BBMAP_CLUMPIFY { conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.98--h5c4e2a8_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.98--h5c4e2a8_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.98--h5c4e2a8_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index c461b0b9eb4..05e1c95295c 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -5,7 +5,7 @@ process BBMAP_INDEX { conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bbmap:38.92--he522d1c_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.92--he522d1c_0" } input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 7c31fbb6509..10ef64dd90e 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -5,7 +5,7 @@ process BBMAP_PILEUP { conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 8e46974eacc..19f007ac8ec 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_ANNOTATE { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 162d1e4a85e..8003dfe556c 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_CONCAT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index d957a493945..c6141e5deba 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_CONSENSUS { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index 5f7c1234d99..ac39db740a0 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 63d05ef631b..6771425dfaf 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_FILTER { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index f49379e274c..b1d5174374b 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_INDEX { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 1801c21e5df..2d8993c72a6 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_ISEC { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 124c41cf98c..80e6ab7654c 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_MERGE { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index cb07045c254..35b1761f170 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_MPILEUP { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 0fba8b9ed7e..5aafaa4dda7 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_NORM { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 82f66c31fa7..8c9011e09ca 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_QUERY { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index c36fdb420c4..47dc7cb3563 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_REHEADER { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 323f27579e3..a7960977493 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_ROH { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index cd39c32d12e..de42b723fd4 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_SORT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 3d9eb0a6dd6..f40c9ac8a8c 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_STATS { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 5a8eabda681..b2ad7a3bcf5 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_VIEW { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index 2d3a1ce155a..ec9cdc7c047 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_BAMTOBED { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index d7b6e457830..e6dbcfbbae7 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_COMPLEMENT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index a40ef1534fd..3872a63bca5 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_GENOMECOV { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 3f753cd5392..5b63ab31ac1 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_GETFASTA { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: path bed diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index de1e05d3087..0903f0290eb 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_INTERSECT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index c097d3aa68b..12e6b65c73e 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_MAKEWINDOWS { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_1" } input: tuple val(meta), path(regions) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index acf928eb90d..fbab190d1aa 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_MASKFASTA { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 615e3257766..1d222502b63 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_MERGE { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index a510b9e0cff..be900f7b5ca 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_SLOP { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index dc61624e237..676a9455eb0 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_SORT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index cfefcb88f66..65487485036 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_SPLIT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h468198e_3': - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_2" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index f39bcdda0f7..63f1f3f8d12 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_SUBTRACT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/modules/nf-core/biobambam/bammarkduplicates2/main.nf index 33c84aa4738..430caa92c14 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -3,7 +3,7 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 { label 'process_medium' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_url ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} + container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index 6d92a5af004..45b146c585a 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -5,7 +5,7 @@ process BIOBAMBAM_BAMMERGE { conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index 95066cead19..59df0bba89e 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -3,7 +3,7 @@ process BIOBAMBAM_BAMSORMADUP { label "process_medium" conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_url ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} + container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} input: tuple val(meta), path(bams, stageAs: "?/*") diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index cac25d9aaee..337c20e501a 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -5,7 +5,7 @@ process BISCUIT_ALIGN { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 2605bf788b0..f44c872dd4a 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -5,7 +5,7 @@ process BISCUIT_BLASTER { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index aac47a75d48..94ae13e837c 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -5,7 +5,7 @@ process BISCUIT_BSCONV { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index 1f9ac0fbd38..93cfcaba4c7 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -5,7 +5,7 @@ process BISCUIT_EPIREAD { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(bam), path(bai), path(snp_bed) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 24755a26992..a41d5a7cbf8 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -5,7 +5,7 @@ process BISCUIT_INDEX { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index 3e38f00d444..95006108419 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -5,7 +5,7 @@ process BISCUIT_MERGECG { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 69daab9aad3..362acbd0533 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -5,7 +5,7 @@ process BISCUIT_PILEUP { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index 38771a969a0..a17eed1db7b 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -5,7 +5,7 @@ process BISCUIT_QC { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 30771e6466e..348b13a96b8 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -5,7 +5,7 @@ process BISCUIT_VCF2BED { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index dcb71b0c7fe..ec9fa8b6feb 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -5,7 +5,7 @@ process BISMARK_ALIGN { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index 19bd159436d..a64a375bf1e 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -5,7 +5,7 @@ process BISMARK_DEDUPLICATE { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index de1136c68ac..2bd7d2d5fe4 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -5,7 +5,7 @@ process BISMARK_GENOMEPREPARATION { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 8a9e42cf3e8..3bb924717f4 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -5,7 +5,7 @@ process BISMARK_METHYLATIONEXTRACTOR { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 1498b638423..449041c0254 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -5,7 +5,7 @@ process BISMARK_REPORT { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index ce2828cddae..ea42ad92bf9 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -4,7 +4,7 @@ process BISMARK_SUMMARY { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: path(bam) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index 78ca59afc1c..1bdb761d1ca 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -5,7 +5,7 @@ process BLAST_BLASTN { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 6aabd511c5b..a03d18706ef 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -5,7 +5,7 @@ process BLAST_MAKEBLASTDB { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 7189502c520..1888c50c0bf 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -5,7 +5,7 @@ process BLAST_TBLASTN { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index a0966cf5651..9557f2ab9a9 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -5,7 +5,7 @@ process BOWTIE_ALIGN { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 0e9abae6cd2..1e51d81010e 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -5,7 +5,7 @@ process BOWTIE_BUILD { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bowtie:1.3.0--py38hed8969a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bowtie:1.3.0--py38hed8969a_1" } input: path fasta diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 0bbd3b0ea45..e28f4fd2421 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -5,7 +5,7 @@ process BOWTIE2_ALIGN { conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) container { workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 67c20960439..a9aabb3a851 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -5,7 +5,7 @@ process BOWTIE2_BUILD { conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bowtie2:2.4.4--py39hbb4e92a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bowtie2:2.4.4--py39hbb4e92a_0" } input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index ac082102b2e..ff6bebec5ca 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -7,7 +7,7 @@ process BRACKEN_BRACKEN { conda (params.enable_conda ? "bioconda::bracken=2.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } input: tuple val(meta), path(kraken_report) diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 439505a948f..41eec2a47e7 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -4,7 +4,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { conda (params.enable_conda ? "bioconda::bracken=2.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index cc94cf75ff5..8c40cfbf261 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -5,7 +5,7 @@ process BUSCO { conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/busco:5.4.3--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/busco:5.4.3--pyhdfd78af_0" } input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 8e587b678a2..4ab817ae171 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -5,7 +5,7 @@ process BWA_ALN { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bwa:0.7.17--h5bf99c6_8" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa:0.7.17--h5bf99c6_8" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 1710d6e0340..1eab7f80231 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -5,7 +5,7 @@ process BWA_INDEX { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bwa:0.7.17--hed695b0_7" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa:0.7.17--hed695b0_7" } input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 1c72dd77788..ee2f04432a8 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -5,7 +5,7 @@ process BWA_MEM { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 4c460bbf71b..9e0535c0836 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -5,7 +5,7 @@ process BWA_SAMPE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index a2112db87f0..2f37920670b 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -5,7 +5,7 @@ process BWA_SAMSE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 2be4347353f..51b38d24ec2 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -5,7 +5,7 @@ process BWAMEM2_INDEX { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bwa-mem2:2.2.1--he513fc3_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa-mem2:2.2.1--he513fc3_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 787e6db9bf6..fa7f7ba9baf 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -5,7 +5,7 @@ process BWAMEM2_MEM { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 925dbc2ada1..c383afe98d6 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -5,7 +5,7 @@ process BWAMETH_ALIGN { conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 2e2f4aff083..84f7b6b1499 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -5,7 +5,7 @@ process BWAMETH_INDEX { conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 3da462e33db..ab5cbc7544c 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -5,7 +5,7 @@ process CAT_CAT { conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pigz:2.3.4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pigz:2.3.4" } input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 59b3968e949..78653e0531d 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -5,7 +5,7 @@ process CENTRIFUGE_CENTRIFUGE { conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : - "${params.docker_url ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 512b7c7583d..541c466143e 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -5,7 +5,7 @@ process CENTRIFUGE_KREPORT { conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': - "${params.docker_url ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index 0e82563b763..c25ad22f71f 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -5,7 +5,7 @@ process CHECKM_LINEAGEWF { conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 9716dfe4126..a52ce2381db 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -5,7 +5,7 @@ process CHECKM_QA { conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index 437624f2dc9..d1b3a883653 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -5,7 +5,7 @@ process CHROMAP_CHROMAP { conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 545e1052911..6bd7c412ee7 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -5,7 +5,7 @@ process CHROMAP_INDEX { conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/chromap:0.2.1--hd03093a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/chromap:0.2.1--hd03093a_0" } input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 9b7d74fd3b6..11df3d331a0 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -5,7 +5,7 @@ process CLONALFRAMEML { conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/clonalframeml:1.12--h7d875b9_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/clonalframeml:1.12--h7d875b9_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/clonalframeml:1.12--h7d875b9_1" } input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index 6cdeabf1a93..a6325206c2b 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -6,7 +6,7 @@ process CMSEQ_POLYMUT { conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cmseq:1.0.4--pyhb7b1952_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cmseq:1.0.4--pyhb7b1952_0" } input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index fc7062a6675..a10699e15c7 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -5,7 +5,7 @@ process CNVKIT_ANTITARGET { conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index f59f255b8d2..680a6d9d7c3 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -5,7 +5,7 @@ process CNVKIT_BATCH { conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" } input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index d98f4b9a7f5..5b656960628 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -5,7 +5,7 @@ process CNVKIT_REFERENCE { conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } input: path fasta diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index 69c1a41568e..2f9909f4d7a 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -5,7 +5,7 @@ process CNVPYTOR_CALLCNVS { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 77788a5db45..a635a291cc9 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -5,7 +5,7 @@ process CNVPYTOR_HISTOGRAM { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index 52419e8e9e8..e0e611e08f7 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -5,7 +5,7 @@ process CNVPYTOR_IMPORTREADDEPTH { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(input_file), path(index) diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index 89ac65f9dd9..d410088735e 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -5,7 +5,7 @@ process CNVPYTOR_PARTITION { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index ad4a1ddee79..dda48698626 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -5,7 +5,7 @@ process CNVPYTOR_VIEW { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor_files) diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index d7050c9e2e7..4d14f15eb2f 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -5,7 +5,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 630d50153ac..7ada37c99dc 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -5,7 +5,7 @@ process CONTROLFREEC_FREEC { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index a9ea2aca7fd..83fd867418f 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -5,7 +5,7 @@ process CONTROLFREEC_FREEC2BED { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index aa2b12f1477..7a51adf7177 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -5,7 +5,7 @@ process CONTROLFREEC_FREEC2CIRCOS { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index cf8ca736d70..b2c5396d4fa 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -5,7 +5,7 @@ process CONTROLFREEC_MAKEGRAPH { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 2d9bd85e9e4..04263becd20 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -5,7 +5,7 @@ process COOLER_CLOAD { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(pairs), path(index) diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index 83f4e35ead9..d18369ef764 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -5,7 +5,7 @@ process COOLER_DIGEST { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: path fasta diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index 4ef275496b7..97d7eb1e706 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -5,7 +5,7 @@ process COOLER_DUMP { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index d442d8a8ae0..cc5fe692dcd 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -5,7 +5,7 @@ process COOLER_MERGE { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 6af32477b9e..56d18f45b07 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -5,7 +5,7 @@ process COOLER_ZOOMIFY { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index 14a1a3a31dd..be08a40306d 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -5,7 +5,7 @@ process CRUMBLE { conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/crumble:0.9.0--hb0d9459_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/crumble:0.9.0--hb0d9459_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/crumble:0.9.0--hb0d9459_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 8d72d097356..4b484418743 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -5,7 +5,7 @@ process CSVTK_CONCAT { conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index f3a1ae7e8d1..838a6750de6 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -5,7 +5,7 @@ process CSVTK_SPLIT { conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index d87ad0c6512..d371f29938a 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -5,7 +5,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 2191a3d6473..ba9b32e91a0 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -5,7 +5,7 @@ process CUSTOM_GETCHROMSIZES { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 7428131097e..6e21c1a4264 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -5,7 +5,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } output: path('*.mkfg') , emit: ncbi_settings diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 95c568cec7c..e5249d5364c 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -5,7 +5,7 @@ process CUTADAPT { conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/cutadapt:3.4--py39h38f01e4_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/cutadapt:3.4--py39h38f01e4_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index 3c26f190c8b..555393f3623 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -5,7 +5,7 @@ process DAMAGEPROFILER { conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/damageprofiler:1.1--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/damageprofiler:1.1--hdfd78af_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index 6c7faa55b27..fd36a7101ca 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -5,7 +5,7 @@ process DASTOOL_DASTOOL { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index 3ee3f8b5103..e6fadb56440 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -5,7 +5,7 @@ process DASTOOL_FASTATOCONTIG2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 6c9b7ed4cd4..226360d0857 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -5,7 +5,7 @@ process DASTOOL_SCAFFOLDS2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/das_tool:1.1.3--r41hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.3--r41hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index 53d73a0d710..be6b51b6085 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -5,7 +5,7 @@ process DEDUP { conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dedup:0.12.8--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dedup:0.12.8--hdfd78af_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index d2c5617701d..4711d6c827d 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -4,7 +4,7 @@ process DEEPARG_DOWNLOADDATA { conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index f7378a6abbf..e019a5321cc 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -5,7 +5,7 @@ process DEEPARG_PREDICT { conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index d978c8677ed..520a5915c28 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -4,7 +4,7 @@ process DEEPBGC_DOWNLOAD { conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index 4c488342694..c576fd3eaec 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -5,7 +5,7 @@ process DEEPBGC_PIPELINE { conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 5275cedf79f..5c8616acdbb 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -5,7 +5,7 @@ process DEEPTOOLS_BAMCOVERAGE { conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 8e91d05d965..15881f3ae18 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -5,7 +5,7 @@ process DEEPTOOLS_COMPUTEMATRIX { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index 3b75edd85c5..f12a855d297 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -5,7 +5,7 @@ process DEEPTOOLS_PLOTFINGERPRINT { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index 3c730dd3a02..d41a8a29620 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -5,7 +5,7 @@ process DEEPTOOLS_PLOTHEATMAP { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index 27ed76e37d8..42c9e6b00fe 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -5,7 +5,7 @@ process DEEPTOOLS_PLOTPROFILE { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index e329f5c4a7f..f47dacb590d 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -5,7 +5,7 @@ process DELLY_CALL { conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/delly:1.1.5--h358d541_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/delly:1.1.5--h358d541_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/delly:1.1.5--h358d541_0" } input: tuple val(meta), path(input), path(input_index), path(exclude_bed) diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index 0651a7833c9..03b7c321e6f 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -5,7 +5,7 @@ process DIAMOND_BLASTP { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index f28abd2ee88..80669546d6b 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -5,7 +5,7 @@ process DIAMOND_BLASTX { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index cc8e1eb5fd0..36ee64346b8 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -5,7 +5,7 @@ process DIAMOND_MAKEDB { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index 7562f64212f..ee18bc73315 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -5,7 +5,7 @@ process DRAGMAP_ALIGN { conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 54e3c531e16..3e6b4f9f4a7 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -5,7 +5,7 @@ process DRAGMAP_HASHTABLE { conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/dragmap:1.2.1--hd4ca14e_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dragmap:1.2.1--hd4ca14e_0" } input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index 16383de2e68..46a9df8d601 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -5,7 +5,7 @@ process DRAGONFLYE { conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dragonflye:1.0.11--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dragonflye:1.0.11--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 095a88600cd..4db716289cc 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -5,7 +5,7 @@ process DSHBIO_EXPORTSEGMENTS { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 7299b4081e9..2d59ce1eed9 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -5,7 +5,7 @@ process DSHBIO_FILTERBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index cba9ed7dfb0..79979781b51 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -5,7 +5,7 @@ process DSHBIO_FILTERGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index 7c256dfaff8..6e6bfc579ff 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -5,7 +5,7 @@ process DSHBIO_SPLITBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 95362f5abb9..da5c3fefba1 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -5,7 +5,7 @@ process DSHBIO_SPLITGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 65bf40fa64d..2fa192208f9 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -5,7 +5,7 @@ process ECTYPER { conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ectyper:1.0.0--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ectyper:1.0.0--pyhdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index fd4f90a7458..e3e1ecbcd8d 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -5,7 +5,7 @@ process ELPREP_FILTER { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index ed4a43a314d..18fb7e1f4a2 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -5,7 +5,7 @@ process ELPREP_MERGE { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index f6eac485321..8141f56bcee 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -5,7 +5,7 @@ process ELPREP_SPLIT { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 431ea6363c8..12a2b73f954 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -5,7 +5,7 @@ process EMBOSS_SEQRET { conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/emboss:6.6.0--hf657eab_5': - "${params.docker_url ?: 'quay.io/biocontainers'}/emboss:6.6.0--h440b012_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/emboss:6.6.0--h440b012_4" } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index dc320ce0518..55b9a2945a7 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -5,7 +5,7 @@ process EMMTYPER { conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/emmtyper:0.2.0--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/emmtyper:0.2.0--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 3a52ba0c963..7fac544df81 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -5,7 +5,7 @@ process ENDORSPY { conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/endorspy:0.4--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/endorspy:0.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/endorspy:0.4--hdfd78af_0" } input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index 22d80ba9e9b..a0df16a9831 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -5,7 +5,7 @@ process ENSEMBLVEP { conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ensembl-vep:106.1--pl5321h4a94de4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ensembl-vep:106.1--pl5321h4a94de4_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 751e72506b9..2a1dde5dc30 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -5,7 +5,7 @@ process ENTREZDIRECT_ESEARCH { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), val(term) diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index 1e5c9138b6c..8325bf636b3 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -5,7 +5,7 @@ process ENTREZDIRECT_ESUMMARY { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), val(uid), path(uids_file) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index bcd7739d8b2..d70da00c417 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -5,7 +5,7 @@ process ENTREZDIRECT_XTRACT { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), path(xml_input) diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index 5f518271298..d7b78f4e4b1 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -5,7 +5,7 @@ process EPANG { conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/epa-ng:0.3.8--h9a82719_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/epa-ng:0.3.8--h9a82719_1" } input: tuple val(meta), path(queryaln) diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index c5bb63aeee4..4dfa99a2763 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -5,7 +5,7 @@ process EXPANSIONHUNTER { conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/expansionhunter:4.0.2--he785bd8_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/expansionhunter:4.0.2--he785bd8_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index 879a47e9f10..ebda89fd069 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -5,7 +5,7 @@ process FAQCS { conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/faqcs%3A2.10--r41h9a82719_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/faqcs:2.10--r41h9a82719_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/faqcs:2.10--r41h9a82719_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index efba5b48dc6..5545d60b3cc 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -6,7 +6,7 @@ process FARGENE { conda (params.enable_conda ? "bioconda::fargene=0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fargene:0.1--py27h21c881e_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fargene:0.1--py27h21c881e_4" } input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index fe61c7852e1..432078d8bcf 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -5,7 +5,7 @@ process FASTANI { conda (params.enable_conda ? "bioconda::fastani=1.32" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fastani:1.32--he1c1bb9_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fastani:1.32--he1c1bb9_0" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index cdf6b80e9d9..01163b73fc8 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -5,7 +5,7 @@ process FASTAWINDOWS { conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/fasta_windows:0.2.4--hec16e2b_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fasta_windows:0.2.4--hec16e2b_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index d3f30095228..32a9c49faf5 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -5,7 +5,7 @@ process FASTP { conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fastp:0.23.2--h79da9fb_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fastp:0.23.2--h79da9fb_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index e26f1c307a1..4cc0c20562a 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -5,7 +5,7 @@ process FASTQC { conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fastqc:0.11.9--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fastqc:0.11.9--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index 272f5da4fc1..bb075099530 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -5,7 +5,7 @@ process FASTQSCAN { conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastq-scan:0.4.4--h7d875b9_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fastq-scan:0.4.4--h7d875b9_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fastq-scan:0.4.4--h7d875b9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 1f0087ebe86..2f38515772c 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -4,7 +4,7 @@ process FASTTREE { conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fasttree:2.1.10--h516909a_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fasttree:2.1.10--h516909a_4" } input: path alignment diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index d30e7c4c795..0be640ec57a 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -5,7 +5,7 @@ process FFQ { conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/ffq:0.2.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ffq:0.2.1--pyhdfd78af_0" } input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index a960f825348..2eb4f59c608 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -5,7 +5,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index 287920c2116..1f0d43b2776 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -5,7 +5,7 @@ process FGBIO_FASTQTOBAM { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 36ab0eca210..2b7788c0f35 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -5,7 +5,7 @@ process FGBIO_GROUPREADSBYUMI { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(taggedbam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index 6c9250e8067..a1f33eea0c6 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -5,7 +5,7 @@ process FGBIO_SORTBAM { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 7828ad02521..600286e1af0 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -5,7 +5,7 @@ process FGBIO_ZIPPERBAMS { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(unmapped_bam) diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index 74c5839d7b3..e016c379f62 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -5,7 +5,7 @@ process FILTLONG { conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/filtlong:0.2.1--h9a82719_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/filtlong:0.2.1--h9a82719_0" } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index 214608f34c6..305605f2174 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -4,7 +4,7 @@ process FLASH { container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/flash:1.2.11--hed695b0_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/flash:1.2.11--hed695b0_5" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 156aee43339..e7ee05e3ed2 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -5,7 +5,7 @@ process FLYE { conda (params.enable_conda ? "bioconda::flye=2.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/flye:2.9--py39h6935b12_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/flye:2.9--py39h6935b12_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index 94a2ada46dd..0d677af1753 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -5,7 +5,7 @@ process FQ_LINT { conda (params.enable_conda ? "bioconda::fq=0.9.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/fq:0.9.1--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/fq:0.9.1--h9ee0642_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 19ed5b56705..7292bc00a56 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -5,7 +5,7 @@ process FREEBAYES { conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/freebayes:1.3.5--py38ha193a2f_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/freebayes:1.3.5--py38ha193a2f_3" } input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 980f2600b53..b2440322f81 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -7,7 +7,7 @@ process GAMMA_GAMMA { conda (params.enable_conda ? "bioconda::gamma=2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gamma:2.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gamma:2.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 86652978380..7d2a81be4ee 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -5,7 +5,7 @@ process GAPPA_EXAMINEASSIGN { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index e35a9f9beb1..6cb7ea4c530 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -5,7 +5,7 @@ process GAPPA_EXAMINEGRAFT { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 11dc37a1a0d..d03dcf4a870 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -5,7 +5,7 @@ process GAPPA_EXAMINEHEATTREE { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 355d1b57a3c..b6b33f8bd19 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -5,7 +5,7 @@ process GATK_INDELREALIGNER { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index d467cf0d38d..e6b674121d9 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -5,7 +5,7 @@ process GATK_REALIGNERTARGETCREATOR { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 7d839d8c790..37da825106d 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -5,7 +5,7 @@ process GATK_UNIFIEDGENOTYPER { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 58bbc212cc3..32182976421 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -5,7 +5,7 @@ process GATK4_APPLYBQSR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 2685f41244f..ac121552a77 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -5,7 +5,7 @@ process GATK4_APPLYVQSR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 0fc04f6114f..9227ffd50bf 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -5,7 +5,7 @@ process GATK4_BASERECALIBRATOR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index e773bbbaac0..73bbf0c9141 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -5,7 +5,7 @@ process GATK4_BEDTOINTERVALLIST { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 4f9dc40f492..60a1041ab4f 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -5,7 +5,7 @@ process GATK4_CALCULATECONTAMINATION { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 66990843cb8..27a70de43ef 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -5,7 +5,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 0a678189d5f..f4a90c19cbb 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -5,7 +5,7 @@ process GATK4_COLLECTREADCOUNTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 4aafd8d68e0..fa1b29d4927 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -5,7 +5,7 @@ process GATK4_COLLECTSVEVIDENCE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index b1f83361e1d..ab1612e75a0 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -5,7 +5,7 @@ process GATK4_COMBINEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 32197c7a790..9a6940fe7b9 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -5,7 +5,7 @@ process GATK4_COMPOSESTRTABLEFILE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index a21cfd3a049..8f8ef70cb2c 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -5,7 +5,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 58b93623e6c..50030dd9b8b 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -5,7 +5,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 2d951b7a440..dd34df4edda 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -5,7 +5,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index f1de0350c61..630915f1dff 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -5,7 +5,7 @@ process GATK4_FASTQTOSAM { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index b10deb59956..91f8567dd49 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -5,7 +5,7 @@ process GATK4_FILTERMUTECTCALLS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 00caac2ecef..39f0bf861c6 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -5,7 +5,7 @@ process GATK4_FILTERVARIANTTRANCHES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 052022bedb6..296c51f73ee 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -5,7 +5,7 @@ process GATK4_GATHERBQSRREPORTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index b0e2593a376..57940d092c4 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -5,7 +5,7 @@ process GATK4_GATHERPILEUPSUMMARIES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index e218fbd7f45..2df87696c91 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -5,7 +5,7 @@ process GATK4_GENOMICSDBIMPORT { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index a380f03cb72..c09640c16fe 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -5,7 +5,7 @@ process GATK4_GENOTYPEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 60585af10ed..3a48ab48fb6 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -5,7 +5,7 @@ process GATK4_GETPILEUPSUMMARIES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 538f6cbe20a..f8383d2caca 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -5,7 +5,7 @@ process GATK4_HAPLOTYPECALLER { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index a0994768d74..62de34e2040 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -5,7 +5,7 @@ process GATK4_INDEXFEATUREFILE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 2067aa642a8..b79d113bf4e 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -5,7 +5,7 @@ process GATK4_INTERVALLISTTOBED { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 8dbd3f9470a..500b3866cb9 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -5,7 +5,7 @@ process GATK4_INTERVALLISTTOOLS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index c472a2e4b30..7de592eba0b 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -5,7 +5,7 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index e2e0d8e4676..33780aa10bb 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -5,7 +5,7 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 349c681aa0b..914ae80cd3d 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -5,7 +5,7 @@ process GATK4_MARKDUPLICATES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 02435f7288d..cf44b267b07 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -5,7 +5,7 @@ process GATK4_MERGEBAMALIGNMENT { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index cf7de937a38..56fde9e1a6a 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -5,7 +5,7 @@ process GATK4_MERGEMUTECTSTATS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 6fd8d1a6887..e968a5de638 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -5,7 +5,7 @@ process GATK4_MERGEVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 93ac3598979..c85dd3654ee 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -5,7 +5,7 @@ process GATK4_MUTECT2 { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index d3b35f81e6d..53f25e3d03f 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -5,7 +5,7 @@ process GATK4_PRINTSVEVIDENCE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 3957f841b29..04f2958f4c8 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -5,7 +5,7 @@ process GATK4_REBLOCKGVCF { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 85f6dbfdd3f..b01314209d3 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -5,7 +5,7 @@ process GATK4_REVERTSAM { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 1c11196f684..b1d0185d435 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -5,7 +5,7 @@ process GATK4_SAMTOFASTQ { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index a49377b12cb..4e3c268b967 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -5,7 +5,7 @@ process GATK4_SELECTVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index 56928a45b13..5cf18cc39c2 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -5,7 +5,7 @@ process GATK4_SPLITINTERVALS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index eb02bacef09..fb89851e5b9 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -5,7 +5,7 @@ process GATK4_SPLITNCIGARREADS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index f6ecc3be40c..df864773c90 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -5,7 +5,7 @@ process GATK4_VARIANTFILTRATION { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index ac6404ff1b5..3972ca9fd82 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -5,7 +5,7 @@ process GATK4_VARIANTRECALIBRATOR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index 4da15f4d4f1..b0d44a4de30 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -5,7 +5,7 @@ process GECCO_RUN { conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gecco:0.9.2--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gecco:0.9.2--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gecco:0.9.2--pyhdfd78af_0" } input: tuple val(meta), path(input), path(hmm) diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 7d9c2fcc837..9f276403ec8 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -5,7 +5,7 @@ process GENMAP_INDEX { conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index c095a1cb5da..d1004e644e2 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -5,7 +5,7 @@ process GENMAP_MAPPABILITY { conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index c3addf98d3a..d1f8a1bcdbe 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -5,7 +5,7 @@ process GENMOD_ANNOTATE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 7090b2f2d19..e9bbce0c20b 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -5,7 +5,7 @@ process GENMOD_COMPOUND { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 5d74ce83d65..13440b27065 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -5,7 +5,7 @@ process GENMOD_MODELS { conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 2dcd229843b..56158ffe2b8 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -5,7 +5,7 @@ process GENMOD_SCORE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index 3f9d42642fc..a126fa221f3 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -5,7 +5,7 @@ process GENOMESCOPE2 { conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': - "${params.docker_url ?: 'quay.io/biocontainers'}/genomescope2:2.0--py310r41hdfd78af_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genomescope2:2.0--py310r41hdfd78af_5" } input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index d2ee076a29d..fbfc51cb0cf 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -5,7 +5,7 @@ process GENOTYPHI_PARSE { conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/genotyphi:1.9.1--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genotyphi:1.9.1--hdfd78af_1" } input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 0dcf3db28af..45fef7b1883 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -5,7 +5,7 @@ process GENRICH { conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/genrich:0.6.1--h5bf99c6_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/genrich:0.6.1--h5bf99c6_1" } input: tuple val(meta), path(treatment_bam) diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index cc9825553ff..e91e0306c61 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -6,7 +6,7 @@ process GFAFFIX { container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gfaffix:0.1.4--hec16e2b_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gfaffix:0.1.4--hec16e2b_0" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 772483ca956..49c11e3764a 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -5,7 +5,7 @@ process GFFREAD { conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gffread:0.12.1--h8b12597_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gffread:0.12.1--h8b12597_0" } input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index aa635f6cf19..8bcd20038b9 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -5,7 +5,7 @@ process GLIMPSE_CHUNK { conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/glimpse-bio:1.1.1--hce55b13_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/glimpse-bio:1.1.1--hce55b13_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index e809d0e7fd6..1dfb295cff4 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -5,7 +5,7 @@ process GLNEXUS { conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/glnexus:1.4.1--h40d77a6_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/glnexus:1.4.1--h40d77a6_0" } input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index 8ca9037f83f..ad9a6cf3d67 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -5,7 +5,7 @@ process GOAT_TAXONSEARCH { conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/goat:0.2.0--h92d785c_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/goat:0.2.0--h92d785c_0" } input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index a8e84257c56..bb0f4ddacd2 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -6,7 +6,7 @@ process GRAPHMAP2_ALIGN { conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index 954434361d9..b2a45aa3f6e 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -4,7 +4,7 @@ process GRAPHMAP2_INDEX { conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index 1356ceddb9a..d7a6a5cdfe8 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -5,7 +5,7 @@ process GSTAMA_COLLAPSE { conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 4ac3e5bc66f..3e201cef285 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -5,7 +5,7 @@ process GSTAMA_MERGE { conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gs-tama:1.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.2--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index f388d4bc9dc..3f4e36d981d 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -5,7 +5,7 @@ process GSTAMA_POLYACLEANUP { conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 743ca09dc3b..840310d624d 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -6,7 +6,7 @@ process GTDBTK_CLASSIFYWF { conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gtdbtk:1.5.0--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gtdbtk:1.5.0--pyhdfd78af_0" } input: tuple val(meta), path("bins/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 5229c0b2689..4aa47658c68 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -4,7 +4,7 @@ process GUBBINS { conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gubbins:3.0.0--py39h5bf99c6_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gubbins:3.0.0--py39h5bf99c6_0" } input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 7d17311a57a..317e3891afd 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -5,7 +5,7 @@ process GUNC_DOWNLOADDB { conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index 41cfac09373..e77b1ac79b6 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -5,7 +5,7 @@ process GUNC_RUN { conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index c8df978af71..d7d2b67ea5f 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -5,7 +5,7 @@ process GVCFTOOLS_EXTRACTVARIANTS { conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gvcftools:0.17.0--he941832_3': - "${params.docker_url ?: 'quay.io/biocontainers'}/gvcftools:0.17.0--he941832_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/gvcftools:0.17.0--he941832_3" } input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 96abdb14d91..211d478db24 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -5,7 +5,7 @@ process HAMRONIZATION_ABRICATE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index bc487074fc0..d772d3d23b2 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -5,7 +5,7 @@ process HAMRONIZATION_AMRFINDERPLUS { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 3cbd143deec..4cd0c4c6138 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -5,7 +5,7 @@ process HAMRONIZATION_DEEPARG { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index c125cf3ff34..f79fa50803e 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -5,7 +5,7 @@ process HAMRONIZATION_FARGENE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index 501a0fbeab1..25d4ef68dfe 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -5,7 +5,7 @@ process HAMRONIZATION_RGI { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index 06ad27c9347..4a722411567 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -4,7 +4,7 @@ process HAMRONIZATION_SUMMARIZE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: path(reports) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index 69a3029df39..47a6d44d26a 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -5,7 +5,7 @@ process HAPLOCHECK { conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/haplocheck:1.3.3--h4a94de4_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/haplocheck:1.3.3--h4a94de4_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 8e6e3e4774e..f24f1c16b60 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -5,7 +5,7 @@ process HAPLOGREP2_CLASSIFY { conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/haplogrep:2.4.0--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/haplogrep:2.4.0--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/haplogrep:2.4.0--hdfd78af_0" } input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index 65cc0d88151..03bd91fefb0 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -6,7 +6,7 @@ process HAPPY_HAPPY { conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index c4eb79716f8..6e2d69399a1 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -6,7 +6,7 @@ process HAPPY_PREPY { conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } input: tuple val(meta), path(vcf), path(bed) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 47f53419002..6561fdc16a5 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -5,7 +5,7 @@ process HICAP { conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hicap:1.0.3--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hicap:1.0.3--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index a3458661157..4943b42ac68 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -5,7 +5,7 @@ process HIFIASM { conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hifiasm:0.15.4--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hifiasm:0.15.4--h2e03b76_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index b165406df29..58d0923d322 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -6,7 +6,7 @@ process HISAT2_ALIGN { conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 81651baed38..2d02adf985e 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -7,7 +7,7 @@ process HISAT2_BUILD { conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } input: path fasta diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index f683efd9fa0..6466c3a4960 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -6,7 +6,7 @@ process HISAT2_EXTRACTSPLICESITES { conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 8640e7d6ab0..b02e0477a03 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -5,7 +5,7 @@ process HMMCOPY_GCCOUNTER { conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 01df3607e6b..4dcb7da4cf6 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -6,7 +6,7 @@ process HMMCOPY_GENERATEMAP { conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 62eaedd2de8..1bbade25e3f 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -5,7 +5,7 @@ process HMMCOPY_MAPCOUNTER { conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 71d9b2746ba..5f4c4b5619b 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -6,7 +6,7 @@ process HMMCOPY_READCOUNTER { conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index 0996adea5f5..c5d86ac3874 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -5,7 +5,7 @@ process HMMER_ESLALIMASK { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index f6bfe7fee90..37e0b9413b0 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -5,7 +5,7 @@ process HMMER_ESLREFORMAT { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 21a2fb32640..2cfdcbb7154 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -5,7 +5,7 @@ process HMMER_HMMALIGN { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 02b50736fe9..b0f5bf37db1 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -5,7 +5,7 @@ process HMMER_HMMBUILD { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 4d81d4ad7ec..f8b45a89578 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -5,7 +5,7 @@ process HMMER_HMMSEARCH { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index d05229644ca..0edecd14478 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -5,7 +5,7 @@ process HMTNOTE { conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hmtnote:0.7.2--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hmtnote:0.7.2--pyhdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 42ec3f4c108..18a064592e8 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -6,7 +6,7 @@ process HOMER_ANNOTATEPEAKS { conda (params.enable_conda ? "bioconda::homer=4.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 23c630ce612..dda9472ae1a 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -6,7 +6,7 @@ process HOMER_FINDPEAKS { conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index d2014cd1392..473a852dbbc 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -7,7 +7,7 @@ process HOMER_MAKETAGDIRECTORY { conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 854d35dd3e3..041b34405f2 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -6,7 +6,7 @@ process HOMER_MAKEUCSCFILE { conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index 12873c7dbb8..e60d7b69298 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -6,7 +6,7 @@ process HOMER_POS2BED { conda (params.enable_conda ? "bioconda::homer=4.11" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 2634dab91a6..684ae576bee 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -6,7 +6,7 @@ process HPSUISSERO { conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/hpsuissero:1.0.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hpsuissero:1.0.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index 47371a78d7a..87759bb5e59 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -5,7 +5,7 @@ process ICHORCNA_CREATEPON { conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } input: path wigs diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index 62b268bebca..c4a5817ddc8 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -6,7 +6,7 @@ process ICHORCNA_RUN { conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index 58370ef9600..0fcdbc3407f 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -5,7 +5,7 @@ process IDR { conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/idr:2.0.4.2--py39hcbe4a3b_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/idr:2.0.4.2--py39hcbe4a3b_5" } input: path peaks diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index 8138a66b9f9..a81fcc47e99 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -5,7 +5,7 @@ process INSTRAIN_PROFILE { conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/instrain:1.6.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/instrain:1.6.1--pyhdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index decb4d34fa6..279bdeb8568 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -5,7 +5,7 @@ process IQTREE { conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/iqtree:2.1.4_beta--hdcc8f71_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/iqtree:2.1.4_beta--hdcc8f71_0" } input: path alignment diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index 4e3599aa902..67bd82b6fa0 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -5,7 +5,7 @@ process ISMAPPER { conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ismapper:2.0.2--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ismapper:2.0.2--pyhdfd78af_1" } input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index 27c69b918d4..167431990e4 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -5,7 +5,7 @@ process ISOSEQ3_CLUSTER { conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index 393a2ffeb7a..3db51a3a414 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -5,7 +5,7 @@ process ISOSEQ3_REFINE { conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index e33580097fb..e84bfdde2a4 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -5,7 +5,7 @@ process IVAR_CONSENSUS { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index 0cc40d92704..89ecbf4886f 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -5,7 +5,7 @@ process IVAR_TRIM { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index bab663e9c16..0327e195261 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -5,7 +5,7 @@ process IVAR_VARIANTS { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index 08dd08837bf..509321b0fa9 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -10,7 +10,7 @@ process JUPYTERNOTEBOOK { conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index 0fb8ca4c660..17bf5aab8cb 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -5,7 +5,7 @@ process KAIJU_KAIJU { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 20c3160a4e7..b95d6c70b74 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -5,7 +5,7 @@ process KAIJU_KAIJU2KRONA { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 9b0c29959d1..83246486030 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -5,7 +5,7 @@ process KAIJU_KAIJU2TABLE { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h2e03b76_0" } input: tuple val(meta), path(results) diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 9c5773c5729..4d06a2ff288 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -5,7 +5,7 @@ process KALLISTO_INDEX { conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/kallisto:0.46.2--h4f7b962_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kallisto:0.46.2--h4f7b962_1" } input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 0a350d71ccd..1ba8e5090f8 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -5,7 +5,7 @@ process KALLISTOBUSTOOLS_COUNT { conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 7d00cd8b942..7184d05e495 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -5,7 +5,7 @@ process KALLISTOBUSTOOLS_REF { conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } input: path fasta diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 29cf554d8cb..c7e67c83869 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -5,7 +5,7 @@ process KAT_HIST { conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/kat:2.4.2--py38hfc5f9d8_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kat:2.4.2--py38hfc5f9d8_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index ce97648961b..8b2eaa0ada2 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -5,7 +5,7 @@ process KHMER_NORMALIZEBYMEDIAN { conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } input: path pe_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index d04df729865..28b24872cae 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -5,7 +5,7 @@ process KHMER_UNIQUEKMERS { conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } input: path fasta diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index 29a6f2393f8..a1e6aef5621 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -5,7 +5,7 @@ process KLEBORATE { conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/kleborate:2.1.0--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/kleborate:2.1.0--pyhdfd78af_1" } input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 980b34723fd..f932b80b1a8 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -5,7 +5,7 @@ process KRAKEN2_KRAKEN2 { conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index 488c91dbaeb..356663493c9 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -4,7 +4,7 @@ process KRAKENTOOLS_COMBINEKREPORTS { conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 9befeec29a2..dd1cdfd4841 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -6,7 +6,7 @@ process KRAKENTOOLS_KREPORT2KRONA { conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index 278270bfcfe..ca78dc179de 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -6,7 +6,7 @@ process KRONA_KRONADB { conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index cb6b4496089..3d9c1311b02 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -6,7 +6,7 @@ process KRONA_KTIMPORTTAXONOMY { conda (params.enable_conda ? "bioconda::krona=2.8" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.8--pl5262hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.8--pl5262hdfd78af_2" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 463c53df5d0..5d432e9942d 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -5,7 +5,7 @@ process KRONA_KTIMPORTTEXT { conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.8.1--pl5321hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.8.1--pl5321hdfd78af_1" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index 16cd3d01e19..d471c0ed537 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -6,7 +6,7 @@ process KRONA_KTUPDATETAXONOMY { conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 614f50cf423..5c03ea61a70 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -5,7 +5,7 @@ process LAST_DOTPLOT { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index a3d25770b2a..b2c5cbe3a9d 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -5,7 +5,7 @@ process LAST_LASTAL { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index b0e282180d1..af991a9b316 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -5,7 +5,7 @@ process LAST_LASTDB { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 57a92cde5df..00c73eacb3a 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -5,7 +5,7 @@ process LAST_MAFCONVERT { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index cad83b254ca..94950c1eea1 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -5,7 +5,7 @@ process LAST_MAFSWAP { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 6333ca8b38f..9feb0863cfb 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -5,7 +5,7 @@ process LAST_POSTMASK { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index a8870ccf093..c2d0fb661a4 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -5,7 +5,7 @@ process LAST_SPLIT { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index bc5b1ed480c..e3460b96d57 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -5,7 +5,7 @@ process LAST_TRAIN { conda (params.enable_conda ? 'bioconda::last=1250' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index b4e6f634f15..befca1facc2 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -6,7 +6,7 @@ process LEEHOM { conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/leehom:1.2.15--h29e30f7_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/leehom:1.2.15--h29e30f7_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index a406b47d401..61bd31a7d00 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -5,7 +5,7 @@ process LEGSTA { conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/legsta:0.5.1--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/legsta:0.5.1--hdfd78af_2" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 10fe343ee06..b8edd60b871 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -5,7 +5,7 @@ process LIMA { conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/lima:2.2.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/lima:2.2.0--h9ee0642_0" } input: tuple val(meta), path(ccs) diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index e33dce314be..72a33213d98 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -5,7 +5,7 @@ process LISSERO { conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/lissero:0.4.9--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/lissero:0.4.9--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index d67a92ec40e..8e4a3c853e0 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -5,7 +5,7 @@ process LOFREQ_CALL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 6502ad20beb..f751d14b8f8 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -5,7 +5,7 @@ process LOFREQ_CALLPARALLEL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index bc7be19a6e7..717bc8a9886 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -5,7 +5,7 @@ process LOFREQ_FILTER { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 12717f8b387..43f1349912d 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -5,7 +5,7 @@ process LOFREQ_INDELQUAL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 5a540eb0b86..17a97bd90e5 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -5,7 +5,7 @@ process MACREL_CONTIGS { conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/macrel:1.1.0--py36hc5360cc_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/macrel:1.1.0--py36hc5360cc_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 50198829160..93979e6057e 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -5,7 +5,7 @@ process MACS2_CALLPEAK { conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/macs2:2.2.7.1--py38h4a8c8d9_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/macs2:2.2.7.1--py38h4a8c8d9_3" } input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index da92735711e..4c886768c3e 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -5,7 +5,7 @@ process MAFFT { conda (params.enable_conda ? "bioconda::mafft=7.490" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mafft:7.490--h779adbc_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mafft:7.490--h779adbc_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 7ba57002bb0..37934fe95f2 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -5,7 +5,7 @@ process MALT_BUILD { conda (params.enable_conda ? "bioconda::malt=0.41" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/malt:0.41--1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/malt:0.41--1" } input: path fastas diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index 03dbc3fbb37..16d0bfb15da 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -5,7 +5,7 @@ process MALT_RUN { conda (params.enable_conda ? "bioconda::malt=0.41" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/malt:0.41--1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/malt:0.41--1" } input: tuple val(meta), path(fastqs) diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index d24ac92c450..8dec64acc80 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -5,7 +5,7 @@ process MALTEXTRACT { conda (params.enable_conda ? "bioconda::hops=0.35" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } input: path rma6 diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 95b87008263..6c11f182c1b 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -5,7 +5,7 @@ process MANTA_CONVERTINVERSION { conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index cdbf38e5da1..1ad8d0d0a31 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -5,7 +5,7 @@ process MANTA_GERMLINE { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index bbd3e3129d5..86971230778 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -5,7 +5,7 @@ process MANTA_SOMATIC { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 8366a83f93d..3641b443c00 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -5,7 +5,7 @@ process MANTA_TUMORONLY { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index 402f292a2bf..14922d998c9 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -5,7 +5,7 @@ process MAPDAMAGE2 { conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mapdamage2:2.2.1--pyr40_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mapdamage2:2.2.1--pyr40_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index a044d569750..f106535abe0 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -5,7 +5,7 @@ process MASH_DIST { conda (params.enable_conda ? "bioconda::mash=2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 913a93679cf..7d90d249bc0 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -5,7 +5,7 @@ process MASH_SCREEN { conda (params.enable_conda ? "bioconda::mash=2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 3a875aa7ad3..ea9050e7c6e 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -4,7 +4,7 @@ process MASH_SKETCH { conda (params.enable_conda ? "bioconda::mash=2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index bd40dcfcd97..4e5a6152f3c 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -5,7 +5,7 @@ process MASHTREE { conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mashtree:1.2.0--pl526h516909a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mashtree:1.2.0--pl526h516909a_0" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index d001a66be44..6a540f9fcc3 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -5,7 +5,7 @@ process MAXBIN2 { conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/maxbin2:2.2.7--he1b5a44_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/maxbin2:2.2.7--he1b5a44_2" } input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index 2bf0f411986..df9060ba5c5 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -5,7 +5,7 @@ process MAXQUANT_LFQ { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" } else { - container ${params.docker_url ?: 'quay.io/biocontainers'}/maxquant:2.0.3.0--py310hdfd78af_1 + container ${params.docker_registry ?: 'quay.io/biocontainers'}/maxquant:2.0.3.0--py310hdfd78af_1 } input: diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index 62d0eaca2e1..d10425c645d 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -6,7 +6,7 @@ process MCRONI { conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mcroni:1.0.4--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mcroni:1.0.4--pyh5e36f6f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index 561d71d4cd0..7e9e42501d7 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -5,7 +5,7 @@ process MEDAKA { conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/medaka:1.4.4--py38h130def0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/medaka:1.4.4--py38h130def0_0" } input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 1017c51eda8..8e5d7512c30 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -5,7 +5,7 @@ process MEGAHIT { conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index 414ef622fa7..d39036d6f5e 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -5,7 +5,7 @@ process MEGAN_DAA2INFO { conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } input: tuple val(meta), path(daa) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index aaf10074064..5dee8eb20b7 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -5,7 +5,7 @@ process MEGAN_RMA2INFO { conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index 452538efedc..78fa9673f2f 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -5,7 +5,7 @@ process MENINGOTYPE { conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/meningotype:0.8.5--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/meningotype:0.8.5--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index 2cf7eb2ce7a..48eeb0424f2 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -5,7 +5,7 @@ process MERQURY { conda (params.enable_conda ? "bioconda::merqury=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/merqury:1.3--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/merqury:1.3--hdfd78af_1" } input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index 8485e228396..6d9804b9237 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -5,7 +5,7 @@ process MERYL_COUNT { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 5a8bd2b09d5..a25bd71fd32 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -5,7 +5,7 @@ process MERYL_HISTOGRAM { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 53084f80bf6..9d6ea617072 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -5,7 +5,7 @@ process MERYL_UNIONSUM { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 830d64c40da..7094cdd332a 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -5,7 +5,7 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index e11a516155e..3f04b8b207c 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -5,7 +5,7 @@ process METABAT2_METABAT2 { conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 221c8da6ad4..64264416674 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -4,7 +4,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 9a439967ccc..7eab1b61a5c 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -5,7 +5,7 @@ process METAPHLAN3_METAPHLAN3 { conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 49d35d02f6e..d6fa47d43fb 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -5,7 +5,7 @@ process METHYLDACKEL_EXTRACT { conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index 399c283205e..65ff7182871 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -5,7 +5,7 @@ process METHYLDACKEL_MBIAS { conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index a7344149370..83a503c7cc0 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -5,7 +5,7 @@ process MINIA { conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/minia:3.2.6--h9a82719_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/minia:3.2.6--h9a82719_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 8410aceb09e..3eb0ebd8dca 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -5,7 +5,7 @@ process MINIASM { conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/miniasm:0.3_r179--h5bf99c6_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/miniasm:0.3_r179--h5bf99c6_2" } input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index 5fc0eede5cf..304da76fbea 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -5,7 +5,7 @@ process MINIMAP2_ALIGN { conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 2e97c2af193..091211d13a1 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -4,7 +4,7 @@ process MINIMAP2_INDEX { conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/minimap2:2.21--h5bf99c6_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/minimap2:2.21--h5bf99c6_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 0f2c6e4a8e5..cd3c8d99cd1 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -5,7 +5,7 @@ process MLST { conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mlst:2.19.0--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mlst:2.19.0--hdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index a434e841b71..312e734b2be 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -5,7 +5,7 @@ process MOBSUITE_RECON { conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mob_suite:3.0.3--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mob_suite:3.0.3--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index ecb8bc7a92f..39f417ac3d8 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -5,7 +5,7 @@ process MOSDEPTH { conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mosdepth:0.3.3--hdfd78af_1"} + "${params.docker_registry ?: 'quay.io/biocontainers'}/mosdepth:0.3.3--hdfd78af_1"} input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index b461e45f6df..984a8042d33 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -4,7 +4,7 @@ process MOTUS_DOWNLOADDB { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index de549938be9..545d48117d2 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -7,7 +7,7 @@ process MOTUS_MERGE { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index 61b088d47cc..4927264b9a8 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -5,7 +5,7 @@ process MOTUS_PROFILE { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index 896ca71873f..e033321fbb0 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -5,7 +5,7 @@ process MSISENSOR_MSI { conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index 520f90fc69b..e9b5c1ea17a 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -5,7 +5,7 @@ process MSISENSOR_SCAN { conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index a9864e71971..e62c4a2e212 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -5,7 +5,7 @@ process MSISENSOR2_MSI { conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index 84a3c7f4e42..9e149368aed 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -5,7 +5,7 @@ process MSISENSOR2_SCAN { conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } input: path fasta diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index f0e7b3375e0..c19eaf3dfa9 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -5,7 +5,7 @@ process MSISENSORPRO_MSI_SOMATIC { conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index bf358fb6008..3e991cabf6c 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -5,7 +5,7 @@ process MSISENSORPRO_SCAN { conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index eb192bce027..d8e5e4f495a 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -5,7 +5,7 @@ process MTNUCRATIO { conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mtnucratio:0.7--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mtnucratio:0.7--hdfd78af_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 8675c2598ee..23aae1e73f4 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,7 +4,7 @@ process MULTIQC { conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 4595770b1a2..1cc277874d6 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -5,7 +5,7 @@ process MULTIVCFANALYZER { conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multivcfanalyzer:0.85.2--hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/multivcfanalyzer:0.85.2--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/multivcfanalyzer:0.85.2--hdfd78af_1" } input: path vcfs diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index f8d21373a75..3eb24606be6 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -6,7 +6,7 @@ process MUMMER { conda (params.enable_conda ? "bioconda::mummer=3.23" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 4c3163f1129..64c5179f637 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -5,7 +5,7 @@ process MUSCLE { conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' : - "${params.docker_url ?: 'quay.io/biocontainers'}/muscle:3.8.1551--h7d875b9_6" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/muscle:3.8.1551--h7d875b9_6" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index 817b1cad2e9..e8f44d9dc2a 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -5,7 +5,7 @@ process MYKROBE_PREDICT { conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/mykrobe:0.11.0--py39h2add14b_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mykrobe:0.11.0--py39h2add14b_1" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 6daf39d3585..e3eb92dd45d 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -5,7 +5,7 @@ process NANOLYSE { conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/nanolyse:1.2.0--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/nanolyse:1.2.0--py_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index 79268beba64..931eca294e9 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -5,7 +5,7 @@ process NANOPLOT { conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/nanoplot:1.40.0--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/nanoplot:1.40.0--pyhdfd78af_0" } input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index d8cd3cda3e0..e8a8538b8d9 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -5,7 +5,7 @@ process NCBIGENOMEDOWNLOAD { conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.1--pyh5e36f6f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ncbi-genome-download:0.3.1--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-genome-download:0.3.1--pyh5e36f6f_0" } input: val meta diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 6dbbae8d49b..1da1ef9ea3f 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -5,7 +5,7 @@ process NEXTCLADE_DATASETGET { conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 5d5ba228c99..b38559680d4 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -5,7 +5,7 @@ process NEXTCLADE_RUN { conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index 39690aae009..d3439ad0e8e 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -5,7 +5,7 @@ process NEXTGENMAP { conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextgenmap%3A0.5.5--hc9558a2_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/nextgenmap:0.5.5--hc9558a2_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/nextgenmap:0.5.5--hc9558a2_4" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index bd3e4b5ea50..8103d9ab7f7 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -5,7 +5,7 @@ process NGMASTER { conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ngmaster:0.5.8--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ngmaster:0.5.8--pyhdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 13aae5cdb13..2e92f85a93e 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -4,7 +4,7 @@ process NGSCHECKMATE_NCM { conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3': - "${params.docker_url ?: 'quay.io/biocontainers'}/ngscheckmate:1.0.0--py27r41hdfd78af_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ngscheckmate:1.0.0--py27r41hdfd78af_3" } input: path files diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index 152a4dadffb..cbb01cd515a 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -5,7 +5,7 @@ process NUCMER { conda (params.enable_conda ? "bioconda::mummer=3.23" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 27815fe5f69..0ae1e2ff5b7 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -5,7 +5,7 @@ process OPTITYPE { conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/optitype:1.3.5--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/optitype:1.3.5--0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index e3a171bd760..f18fdff5992 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -5,7 +5,7 @@ process PAIRIX { conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairix:0.3.7--py36h30a8e3e_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairix:0.3.7--py36h30a8e3e_3" } input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 157c8f54655..32497d0d1c2 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -5,7 +5,7 @@ process PAIRTOOLS_DEDUP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 260ae3d54e8..aa36c98220b 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -5,7 +5,7 @@ process PAIRTOOLS_FLIP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 8e31fe2234d..3d3d6c217ae 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -5,7 +5,7 @@ process PAIRTOOLS_PARSE { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 0ca6f4178d6..33f06b984de 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -5,7 +5,7 @@ process PAIRTOOLS_RESTRICT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(pairs) diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index aa969b838dd..ac35659f4b1 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -5,7 +5,7 @@ process PAIRTOOLS_SELECT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index 8fea7111cd8..383c8be3f94 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -5,7 +5,7 @@ process PAIRTOOLS_SORT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index ed819d925c2..2b1db0eb0cf 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -5,7 +5,7 @@ process PANAROO_RUN { conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/panaroo:1.2.9--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/panaroo:1.2.9--pyhdfd78af_0" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index fd630c28eb5..b7724daf80a 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -5,7 +5,7 @@ process PANGOLIN { conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pangolin:4.1.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pangolin:4.1.1--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index 80a1a80ed6a..a70b25c988d 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -6,7 +6,7 @@ process PARACLU { conda (params.enable_conda ? "bioconda::paraclu=10" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/paraclu:10--h9a82719_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/paraclu:10--h9a82719_1" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 3fb34d750f7..3825912c61c 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -5,7 +5,7 @@ process PASTY { conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pasty:1.0.0--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/pasty:1.0.0--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pasty:1.0.0--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index dd4635e4315..981037e0c60 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -5,7 +5,7 @@ process PBBAM_PBMERGE { conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pbbam:1.7.0--h058f120_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pbbam:1.7.0--h058f120_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 52ec2dbda91..8e73654b88e 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -5,7 +5,7 @@ process PBCCS { conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pbccs:6.2.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pbccs:6.2.0--h9ee0642_0" } input: tuple val(meta), path(bam), path(pbi) diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 86e7401017f..73fe4dd9e9b 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -5,7 +5,7 @@ process PBPTYPER { conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbptyper:1.0.2--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/pbptyper:1.0.2--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pbptyper:1.0.2--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index 44fdf8d991d..c50dd521b44 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -5,7 +5,7 @@ process PEAR { conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pear:0.9.6--h67092d7_8': - "${params.docker_url ?: 'quay.io/biocontainers'}/pear:0.9.6--h67092d7_8" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pear:0.9.6--h67092d7_8" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index d61ab718f22..a93a89a1421 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -5,7 +5,7 @@ process PEDDY { conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/peddy:0.4.8--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/peddy:0.4.8--pyh5e36f6f_0" } input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 2ca314c84b5..ffedc40eccd 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -6,7 +6,7 @@ process PHANTOMPEAKQUALTOOLS { conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/phantompeakqualtools:1.2.2--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/phantompeakqualtools:1.2.2--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index c772e93d7c4..bd6d25c3a9a 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -5,7 +5,7 @@ process PHYLOFLASH { conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/phyloflash:3.4--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/phyloflash:3.4--hdfd78af_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index acfdaf5ee32..dc23e2d93ab 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -5,7 +5,7 @@ process PICARD_ADDORREPLACEREADGROUPS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index e0d2309ea75..dd67a6f658a 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -5,7 +5,7 @@ process PICARD_CLEANSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 85865a7d912..a69ea88af7b 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -5,7 +5,7 @@ process PICARD_COLLECTHSMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index c39173d6d56..60f6baa344c 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -5,7 +5,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index d4483f2568d..db5f7d06fc2 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -5,7 +5,7 @@ process PICARD_COLLECTWGSMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 1b70e32d943..60cbab12492 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -5,7 +5,7 @@ process PICARD_CREATESEQUENCEDICTIONARY { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index 12581a4fc39..4d7165fcf96 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -5,7 +5,7 @@ process PICARD_CROSSCHECKFINGERPRINTS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(input1) diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index 552933a1aec..d8c679b3e94 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -5,7 +5,7 @@ process PICARD_FASTQTOSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index 9c416217562..380b6093a47 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -5,7 +5,7 @@ process PICARD_FILTERSAMREADS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index 7a488cafe7c..97fa949a32b 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -5,7 +5,7 @@ process PICARD_FIXMATEINFORMATION { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 7009bfee90f..9867cb5171f 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -5,7 +5,7 @@ process PICARD_LIFTOVERVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 3d63babcb5c..27810e6c4d6 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -5,7 +5,7 @@ process PICARD_MARKDUPLICATES { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 83a0d41af1f..ad4958a9095 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -5,7 +5,7 @@ process PICARD_MERGESAMFILES { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index ccba0c44447..ca3b30c979a 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -6,7 +6,7 @@ process PICARD_RENAMESAMPLEINVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 5305e44b65f..4a7c888cea3 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -5,7 +5,7 @@ process PICARD_SORTSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index faf2aac260e..eeccdf448ca 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -5,7 +5,7 @@ process PICARD_SORTVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index db2191e3c19..b7d35925169 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -5,7 +5,7 @@ process PINTS_CALLER { conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pypints:1.1.6--pyh5e36f6f_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pypints:1.1.6--pyh5e36f6f_1" } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index c71d1d22ec3..67bff2c7e5b 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -5,7 +5,7 @@ process PIRATE { conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pirate:1.0.4--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pirate:1.0.4--hdfd78af_2" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index b286616303c..a39f0ddc33c 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -6,7 +6,7 @@ process PLASMIDFINDER { conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/plasmidfinder:2.1.6--py310hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plasmidfinder:2.1.6--py310hdfd78af_1" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index d47b0586c9a..7d3cb223978 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -5,7 +5,7 @@ process PLASMIDID { conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/plasmidid:1.6.5--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plasmidid:1.6.5--hdfd78af_0" } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index c9c22ae8192..055cdda2805 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -5,7 +5,7 @@ process PLINK_EXTRACT { conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index edf94a0414b..d4dbd78ed88 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -5,7 +5,7 @@ process PLINK_VCF { conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index 72cd40b600c..e26b99b5a55 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -5,7 +5,7 @@ process PLINK2_EXTRACT { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index b807d17e7fe..1dc58e77823 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -5,7 +5,7 @@ process PLINK2_SCORE { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(pgen), path(psam), path(pvar) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index ce2a48b0cd9..545842f5868 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -5,7 +5,7 @@ process PLINK2_VCF { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 3bb727fb775..506780311f1 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -5,7 +5,7 @@ process PMDTOOLS_FILTER { conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pmdtools:0.60--hdfd78af_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pmdtools:0.60--hdfd78af_5" } input: tuple val(meta), path(bam), path (bai) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index e9a54cb2f12..40c4080f0d5 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -5,7 +5,7 @@ process PORECHOP { conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/porechop:0.2.4--py39h7cff6ad_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/porechop:0.2.4--py39h7cff6ad_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 1f58d2689a5..a19e60f4258 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -6,7 +6,7 @@ process PRESEQ_CCURVE { conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 260651f5646..6706b12e784 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -6,7 +6,7 @@ process PRESEQ_LCEXTRAP { conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index 1fbdb2b33a6..f7d56b026d5 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -5,7 +5,7 @@ process PRINSEQPLUSPLUS { conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/prinseq-plus-plus:1.2.3--hc90279e_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/prinseq-plus-plus:1.2.3--hc90279e_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 4cb57f033fb..ed3f2ccd1fc 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -5,7 +5,7 @@ process PRODIGAL { conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 6be25899cc8..6e78b8d7ac8 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -5,7 +5,7 @@ process PROKKA { conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/prokka:1.14.6--pl5321hdfd78af_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/prokka:1.14.6--pl5321hdfd78af_4" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index 420567618c3..ebcc16592f8 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -5,7 +5,7 @@ process PYCOQC { conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pycoqc:2.5.2--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pycoqc:2.5.2--py_0" } input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index d23425dbc79..223b9211ac0 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -5,7 +5,7 @@ process PYDAMAGE_ANALYZE { conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index a301a0a2184..4f75101b99b 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -5,7 +5,7 @@ process PYDAMAGE_FILTER { conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 5f00302561f..40ab2bddacb 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -5,7 +5,7 @@ process QCAT { conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/qcat:1.1.0--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/qcat:1.1.0--py_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index dfb2a72d74e..838f15045c4 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -5,7 +5,7 @@ process QUALIMAP_BAMQC { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 4a3876c7a15..9efbf028117 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -5,7 +5,7 @@ process QUALIMAP_BAMQCCRAM { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" } input: tuple val(meta), path(cram), path(crai) diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 8f6714a3c2d..6e8f39fb857 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -5,7 +5,7 @@ process QUALIMAP_RNASEQ { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index 7fa153a7748..3f16ba3eb46 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -4,7 +4,7 @@ process QUAST { conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/quast:5.2.0--py39pl5321h2add14b_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/quast:5.2.0--py39pl5321h2add14b_1" } input: path consensus diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index 8a0f9446406..79381cd2104 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -5,7 +5,7 @@ process RACON { conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/racon:1.4.20--h9a82719_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/racon:1.4.20--h9a82719_1" } input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 35cdb758469..f71cb937fc5 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -5,7 +5,7 @@ process RAPIDNJ { conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" } input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 5605e292c3b..7d3583ac824 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -5,7 +5,7 @@ process RASUSA { conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rasusa:0.3.0--h779adbc_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rasusa:0.3.0--h779adbc_1" } input: tuple val(meta), path(reads), val(genome_size) diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index b8187eb5bbb..843c43ab952 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -5,7 +5,7 @@ process RAVEN { conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/raven-assembler:1.6.1--h2e03b76_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/raven-assembler:1.6.1--h2e03b76_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/raven-assembler:1.6.1--h2e03b76_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index 1760e2a6b40..44d3909378c 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -4,7 +4,7 @@ process RAXMLNG { conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/raxml-ng:1.0.3--h32fcf60_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/raxml-ng:1.0.3--h32fcf60_0" } input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 459996af325..9ba82b0abdc 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -5,7 +5,7 @@ process RGI_MAIN { conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/rgi:5.2.1--pyha8f3691_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rgi:5.2.1--pyha8f3691_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index df59e23a976..99382e90062 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -5,7 +5,7 @@ process RHOCALL_ANNOTATE { conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/rhocall:0.5.1--py39hbf8eff0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rhocall:0.5.1--py39hbf8eff0_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 46eb80b9527..9ee4dcf1e6e 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -10,7 +10,7 @@ process RMARKDOWNNOTEBOOK { conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index d9e1947e05c..60c3df3bf99 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -5,7 +5,7 @@ process ROARY { conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/roary:3.13.0--pl526h516909a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/roary:3.13.0--pl526h516909a_0" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 0f466078c33..8792059dbc6 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -5,7 +5,7 @@ process RSEM_CALCULATEEXPRESSION { conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index f286a172ef2..1d863f103c7 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -5,7 +5,7 @@ process RSEM_PREPAREREFERENCE { conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } input: path fasta, stageAs: "rsem/*" diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index c6620b7ed8b..ec35a4387c7 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -5,7 +5,7 @@ process RSEQC_BAMSTAT { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index ee130c73b47..3ed093da97c 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -5,7 +5,7 @@ process RSEQC_INFEREXPERIMENT { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index e2a703375ff..873c74fa705 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -5,7 +5,7 @@ process RSEQC_INNERDISTANCE { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index c21a48c3ae5..d4f2db5cd92 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -5,7 +5,7 @@ process RSEQC_JUNCTIONANNOTATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index cacd49d154e..36c70dd3bdc 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -5,7 +5,7 @@ process RSEQC_JUNCTIONSATURATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index 2174342505b..0098e516753 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -5,7 +5,7 @@ process RSEQC_READDISTRIBUTION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 7885bd94ec1..d50ddd5d772 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -5,7 +5,7 @@ process RSEQC_READDUPLICATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index dd04384675b..984abbe1d3b 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -5,7 +5,7 @@ process RSEQC_TIN { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 6e5d2a81c3f..6b672a53665 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -5,7 +5,7 @@ process RTGTOOLS_PEDFILTER { conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 2f05283b7d6..e1c6749c2d0 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -5,7 +5,7 @@ process RTGTOOLS_VCFEVAL { conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 3f76ddec490..2923582c45c 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -5,7 +5,7 @@ process SALMON_INDEX { conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } input: path genome_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 8ed4acdee0b..f7aec3c8cac 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -5,7 +5,7 @@ process SALMON_QUANT { conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 0d0f8b20f7f..9e1a259d5bd 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -5,7 +5,7 @@ process SAMBLASTER { conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index dd00705f44e..7b461e833a6 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_AMPLICONCLIP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index bb67229f7bd..203762282e8 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_BAM2FQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index a9fdff834d3..490a7deaaa6 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_COLLATE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 00fb07f92b0..b1ed5f26a79 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_COLLATEFASTQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index eb5ee60f59f..ef187b91d04 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index eb114e57a49..09498928c6b 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_DEPTH { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 4b46a2f27ad..4db56870c22 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_DICT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 45e3943cb42..f72a6f90c58 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_FAIDX { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 22508240a82..3e5d84ab342 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_FASTA { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index fc6798598f9..a6f1b7d366d 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_FASTQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index bd31c741b76..51faa31d6cb 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_FIXMATE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 2024239c1a5..b90e81decfc 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_FLAGSTAT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index fe6adb87c82..6a90e259316 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_GETRG { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 8fdee9f041c..d6321b145fa 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_IDXSTATS { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index c3dd5fe3bcd..7423026fefe 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_INDEX { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 80976147f96..dcc05517ef0 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_MARKDUP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 03df854a89a..d3cc2fe289b 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_MERGE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index 115e7a224e0..dc446040945 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_MPILEUP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 5cfe8fbb821..c3e08630920 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_SORT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 28f6de03b92..885f9e337bc 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_STATS { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index c1c6f4457f2..97798e55bd8 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_VIEW { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index 115e577fecf..03397ce622f 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -5,7 +5,7 @@ process SCOARY { conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/scoary:1.6.16--py_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/scoary:1.6.16--py_2" } input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index 18bf627c196..fa0f653736a 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -5,7 +5,7 @@ process SCRAMBLE_CLUSTERANALYSIS { conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } input: tuple val(meta), path(clusters) diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index de6cedf008e..3c70e113e50 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -5,7 +5,7 @@ process SCRAMBLE_CLUSTERIDENTIFIER { conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index 2a57a4a35a1..8f0ca170369 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -6,7 +6,7 @@ process SEACR_CALLPEAK { conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" } input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 126d520c46a..85051e25e6d 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -5,7 +5,7 @@ process SEQKIT_PAIR { conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index b20eb1d64c9..180b60a4786 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -5,7 +5,7 @@ process SEQKIT_REPLACE { conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index d66ce529a09..d2181270ece 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -5,7 +5,7 @@ process SEQKIT_SPLIT2 { conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index f11461498d8..646b8009535 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -5,7 +5,7 @@ process SEQKIT_STATS { conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/seqkit:2.2.0--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.2.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index ee1083ce961..860e35a553a 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -5,7 +5,7 @@ process SEQSERO2 { conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqsero2:1.2.1--py_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqsero2:1.2.1--py_0" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 04368f8ac84..a06dbf3ed15 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -5,7 +5,7 @@ process SEQTK_MERGEPE { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index 44b58d3923a..5123649b746 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -5,7 +5,7 @@ process SEQTK_RENAME { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index c3882b2c0d9..b468aa6c0b5 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -5,7 +5,7 @@ process SEQTK_SAMPLE { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 4b78d45c2b7..8c0d2b187f7 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -5,7 +5,7 @@ process SEQTK_SEQ { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 4a2270bcff9..1f8dfcc11c9 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -5,7 +5,7 @@ process SEQTK_SUBSEQ { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: path sequences diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index 8d1b52fc602..e444ec8b5b1 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -5,7 +5,7 @@ process SEQUENZAUTILS_BAM2SEQZ { conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } input: tuple val(meta), path(normalbam), path(tumourbam) diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 6cd8062aeb8..0a82e63b7f6 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -5,7 +5,7 @@ process SEQUENZAUTILS_GCWIGGLE { conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 137bd8f935b..5b8b2b4a376 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -6,7 +6,7 @@ process SEQWISH_INDUCE { container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/seqwish:0.7.6--h5b5514e_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seqwish:0.7.6--h5b5514e_1" } input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 68bad5959af..1011ac61e7e 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -5,7 +5,7 @@ process SEROBA_RUN { conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/seroba:1.0.2--pyhdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/seroba:1.0.2--pyhdfd78af_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index 450b7bd64da..442b6932700 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -5,7 +5,7 @@ process SEXDETERRMINE { conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/sexdeterrmine:1.1.2--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sexdeterrmine:1.1.2--hdfd78af_1" } input: tuple val(meta), path(depth) diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 9ae4f4c6543..f69be526e95 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -5,7 +5,7 @@ process SHASTA { conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shasta:0.8.0--h7d875b9_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/shasta:0.8.0--h7d875b9_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/shasta:0.8.0--h7d875b9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index 1c3916d9d5b..b41f3d2c5fa 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -5,7 +5,7 @@ process SHIGATYPER { conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/shigatyper:2.0.1--pyhdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/shigatyper:2.0.1--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 6c92bbab0b5..858c7362f2e 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -5,7 +5,7 @@ process SHOVILL { conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/shovill:1.1.0--0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/shovill:1.1.0--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index ae318feaa8f..009f55b0edc 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -5,7 +5,7 @@ process SISTR { conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/sistr_cmd:1.1.1--pyh864c0ab_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sistr_cmd:1.1.1--pyh864c0ab_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index d0fc23653bf..0acfd9b019e 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -6,7 +6,7 @@ process SLIMFASTQ { conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/slimfastq:2.04--h87f3376_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/slimfastq:2.04--h87f3376_2" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index 423d880263a..b25286c2d39 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -5,7 +5,7 @@ process SNAPALIGNER_ALIGN { conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index e8f8d482165..5aaea6bd589 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -5,7 +5,7 @@ process SNAPALIGNER_INDEX { conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } input: path fasta diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index 895d230050b..6b090874fa2 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -5,7 +5,7 @@ process SNIPPY_CORE { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_1" } input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index dbeb629dea5..49d331d6edb 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -5,7 +5,7 @@ process SNIPPY_RUN { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 1b673d7a7b7..30db8333597 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -5,7 +5,7 @@ process SNPDISTS { conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/snp-dists:0.8.2--h5bf99c6_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snp-dists:0.8.2--h5bf99c6_0" } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 4397aafc5fb..6a357bcc761 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -5,7 +5,7 @@ process SNPEFF { conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/snpeff:5.1--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snpeff:5.1--hdfd78af_2" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index 3c7eb901550..a034eb3e103 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -5,7 +5,7 @@ process SNPSIFT_SPLIT { conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/snpsift:4.3.1t--hdfd78af_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snpsift:4.3.1t--hdfd78af_3" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index aaf56400b57..830e7eba4d8 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -4,7 +4,7 @@ process SNPSITES { conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/snp-sites:2.5.1--hed695b0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/snp-sites:2.5.1--hed695b0_0" } input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 05f285a80ad..ce8934cfdbe 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -6,7 +6,7 @@ process SOMALIER_EXTRACT { conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index 890c8fc516b..d533f0413e2 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -6,7 +6,7 @@ process SOMALIER_RELATE { conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } input: tuple val(meta), path(extract) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 31e299c76a6..729c8cc9d79 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -5,7 +5,7 @@ process SORTMERNA { conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/sortmerna:4.3.4--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sortmerna:4.3.4--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index 1afc834817f..4213365ee72 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -5,7 +5,7 @@ process SOURMASH_SKETCH { conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/sourmash:4.2.4--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sourmash:4.2.4--hdfd78af_0" } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 2c1cd19c8f9..85277cc69c9 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -5,7 +5,7 @@ process SPADES { conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/spades:3.15.4--h95f258a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/spades:3.15.4--h95f258a_0" } input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index 463ddf2ec4c..d32977bb050 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -5,7 +5,7 @@ process SPATYPER { conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/spatyper:0.3.3--pyhdfd78af_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/spatyper:0.3.3--pyhdfd78af_3" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index 539e52777bd..cb90aa49d66 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -5,7 +5,7 @@ process SRATOOLS_FASTERQDUMP { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" } input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index dbf25e77f16..880e192b5f2 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -5,7 +5,7 @@ process SRATOOLS_PREFETCH { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } input: tuple val(meta), val(id) diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index c34102c88e4..808ec931b0d 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -5,7 +5,7 @@ process SRST2_SRST2 { conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/srst2:0.2.0--py27_2"} + "${params.docker_registry ?: 'quay.io/biocontainers'}/srst2:0.2.0--py27_2"} input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 348fba4d9a8..009f790ac7f 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -6,7 +6,7 @@ process SSUISSERO { conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/ssuissero:1.0.1--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ssuissero:1.0.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index b707675b953..c79f243508f 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -5,7 +5,7 @@ process STADENIOLIB_SCRAMBLE { conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/staden_io_lib:1.14.14--h0d9da7e_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/staden_io_lib:1.14.14--h0d9da7e_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index 82b76972f3e..adae664f69f 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -5,7 +5,7 @@ process STAPHOPIASCCMEC { conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/staphopia-sccmec:1.0.0--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/staphopia-sccmec:1.0.0--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 365d6da2d32..1ee35253c97 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -5,7 +5,7 @@ process STAR_ALIGN { conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index b4551be3bea..eab9eb5ea70 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -5,7 +5,7 @@ process STAR_GENOMEGENERATE { conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } input: path fasta diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index de4e3dbe150..2e7b25ec9ea 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -5,7 +5,7 @@ process STRANGER { conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/stranger:0.8.1--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/stranger:0.8.1--pyh5e36f6f_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index d47b9f15df8..4c93da9b122 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -5,7 +5,7 @@ process STRELKA_GERMLINE { conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 7ca59636205..1dbf05d39cd 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -5,7 +5,7 @@ process STRELKA_SOMATIC { conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index cf9e193e7b8..9179f064bc4 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -5,7 +5,7 @@ process STRINGTIE_MERGE { conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 2a70a04e909..22832bca83c 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -5,7 +5,7 @@ process STRINGTIE_STRINGTIE { conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 20d2ec8c841..c127b835841 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -5,7 +5,7 @@ process SUBREAD_FEATURECOUNTS { conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/subread:2.0.1--hed695b0_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/subread:2.0.1--hed695b0_0" } input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index e19ee1fa13b..bc65805dfab 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -4,7 +4,7 @@ process SVDB_MERGE { conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" } input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 6200338ce01..75658e642e0 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -5,7 +5,7 @@ process SVDB_QUERY { conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/svdb:2.6.1--py39h5371cbf_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/svdb:2.6.1--py39h5371cbf_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index e2e95049db7..ebdb360f876 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -5,7 +5,7 @@ process SVTK_STANDARDIZE { conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/svtk:0.0.20190615--py37h73a75cf_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/svtk:0.0.20190615--py37h73a75cf_2" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 70fbf2165e6..78ad2aa827f 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -5,7 +5,7 @@ process TABIX_BGZIP { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index bdd6ab6db72..ded6e9d0df3 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -5,7 +5,7 @@ process TABIX_BGZIPTABIX { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index e91a8a6d937..fbd387731f4 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -5,7 +5,7 @@ process TABIX_TABIX { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 09ce7c1d7b8..a8f53f39d9d 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -5,7 +5,7 @@ process TAILFINDR { conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" } input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index f118308e40f..15f53676e23 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -5,7 +5,7 @@ process TBPROFILER_PROFILE { conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/tb-profiler:3.0.8--pypyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/tb-profiler:3.0.8--pypyh5e36f6f_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 3efd0107872..adcf8c4f5e3 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -5,7 +5,7 @@ process TIDDIT_COV { conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/tiddit:3.0.0--py39h59fae87_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/tiddit:3.0.0--py39h59fae87_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 6d7b0f01202..0ad585463a5 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -5,7 +5,7 @@ process TIDDIT_SV { conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/tiddit:3.1.0--py39h59fae87_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/tiddit:3.1.0--py39h59fae87_1" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index cf96c35b54e..6afbce140bf 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -5,7 +5,7 @@ process TRIMGALORE { conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/trim-galore:0.6.7--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/trim-galore:0.6.7--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 55b3f23373b..81c15901e8f 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -5,7 +5,7 @@ process TRIMMOMATIC { conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2': - "${params.docker_url ?: 'quay.io/biocontainers'}/trimmomatic:0.39--hdfd78af_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/trimmomatic:0.39--hdfd78af_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index 86519b6aca3..e9c3d6fd08e 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -6,7 +6,7 @@ process UCSC_BEDCLIP { conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bedclip:377--h0b8a92a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedclip:377--h0b8a92a_2" } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 14ab6a813f8..d5c6cb763e7 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -6,7 +6,7 @@ process UCSC_BEDGRAPHTOBIGWIG { conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bedgraphtobigwig:377--h446ed27_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedgraphtobigwig:377--h446ed27_1" } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index 8ea62b4af02..a84ebb07c5d 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -6,7 +6,7 @@ process UCSC_BEDTOBIGBED { conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--ha8a8165_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bedtobigbed:377--ha8a8165_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedtobigbed:377--ha8a8165_3" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index 676fcde8477..b6e078d6396 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -6,7 +6,7 @@ process UCSC_BIGWIGAVERAGEOVERBED { conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index 082469a6366..69defb4139f 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -6,7 +6,7 @@ process UCSC_LIFTOVER { conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-liftover:377--h0b8a92a_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-liftover:377--h0b8a92a_3" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 73603f90e64..972bcb6e795 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -6,7 +6,7 @@ process UCSC_WIGTOBIGWIG { conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ucsc-wigtobigwig:377--h0b8a92a_2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-wigtobigwig:377--h0b8a92a_2" } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index f5e32f54610..00505e47ba0 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -5,7 +5,7 @@ process ULTRA_ALIGN { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index abf40c565bf..e6897c4ba40 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -5,7 +5,7 @@ process ULTRA_INDEX { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } input: path fasta diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index efb78371d7b..c1ceb5ea5b4 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -5,7 +5,7 @@ process ULTRA_PIPELINE { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 36669cbc310..d508818f1e4 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -5,7 +5,7 @@ process UMITOOLS_DEDUP { conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index f8a3e3c8c71..5c171b80c57 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -5,7 +5,7 @@ process UMITOOLS_EXTRACT { conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index 3d42fca8ef5..c7d151ffd15 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -5,7 +5,7 @@ process UNICYCLER { conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : - "${params.docker_url ?: 'quay.io/biocontainers'}/unicycler:0.4.8--py38h8162308_3" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/unicycler:0.4.8--py38h8162308_3" } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 230a6469971..5c7d473013a 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -5,7 +5,7 @@ process UNZIP { conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/p7zip:15.09--h2d50403_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/p7zip:15.09--h2d50403_4" } input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index b72eda3df1f..b2753e55988 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -5,7 +5,7 @@ process VARDICTJAVA { conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/vardict-java:1.8.3--hdfd78af_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vardict-java:1.8.3--hdfd78af_0" } input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 5a86083bc74..6e4ca4749ae 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -6,7 +6,7 @@ process VARIANTBAM { conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' : - "${params.docker_url ?: 'quay.io/biocontainers'}/variantbam:1.4.4a--h7d7f7ad_5" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/variantbam:1.4.4a--h7d7f7ad_5" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 617ce8cd08f..19e081efcb2 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -6,7 +6,7 @@ process VCF2DB { conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/vcf2db:2020.02.24--hdfd78af_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2db:2020.02.24--hdfd78af_1" } input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 3c15533a3cc..9d4b37a8067 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -7,7 +7,7 @@ process VCF2MAF { conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0': - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" } input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 7cb1b6e5c23..840bd176784 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -5,7 +5,7 @@ process VCFANNO { conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/vcfanno:0.3.3--h9ee0642_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vcfanno:0.3.3--h9ee0642_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index dd7fab79b15..2d2ddb12f25 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -5,7 +5,7 @@ process VCFLIB_VCFBREAKMULTI { conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/vcflib:1.0.3--ha025227_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vcflib:1.0.3--ha025227_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index e8ff0b1afe9..f7c7f4f03b3 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -6,7 +6,7 @@ process VCFLIB_VCFUNIQ { conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/vcflib:1.0.3--hecb563c_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vcflib:1.0.3--hecb563c_1" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index eff434128e0..a987d733438 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -5,7 +5,7 @@ process VCFTOOLS { conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : - "${params.docker_url ?: 'quay.io/biocontainers'}/vcftools:0.1.16--he513fc3_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vcftools:0.1.16--he513fc3_4" } input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 226b79d1367..fdf8d3e9b7a 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -5,7 +5,7 @@ process VERIFYBAMID_VERIFYBAMID2 { conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : - "${params.docker_url ?: 'quay.io/biocontainers'}/verifybamid2:2.0.1--h19d48f6_8" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/verifybamid2:2.0.1--h19d48f6_8" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 44aefc3cf4f..f1953e98cd4 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -5,7 +5,7 @@ process VSEARCH_SINTAX { conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index 8b432a0b534..857fdbf08e8 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -5,7 +5,7 @@ process VSEARCH_USEARCHGLOBAL { conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - "${params.docker_url ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index 63d01ff4889..b2f6b62fdf2 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -5,7 +5,7 @@ process WGSIM { conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/wgsim:1.0--h5bf99c6_4': - "${params.docker_url ?: 'quay.io/biocontainers'}/wgsim:1.0--h5bf99c6_4" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/wgsim:1.0--h5bf99c6_4" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index 18eeec34eba..104f70663b2 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -5,7 +5,7 @@ process WHAMG { conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1': - "${params.docker_url ?: 'quay.io/biocontainers'}/wham:1.8.0.1.2017.05.03--h8b12597_1" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/wham:1.8.0.1.2017.05.03--h8b12597_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index b8cbddec1d3..a4c5e7c106b 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -5,7 +5,7 @@ process YARA_INDEX { conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' : - "${params.docker_url ?: 'quay.io/biocontainers'}/yara:1.0.2--2" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/yara:1.0.2--2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 038c04e7b70..730f8ea7da8 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -5,7 +5,7 @@ process YARA_MAPPER { conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : - "${params.docker_url ?: 'quay.io/biocontainers'}/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" } + "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" } input: tuple val(meta), path(reads) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index ce32a52136d..31d29fb6a7d 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -3,7 +3,7 @@ params { publish_dir_mode = "copy" enable_conda = false singularity_pull_docker_container = false - docker_url = "public.ecr.aws/biocontainers" + docker_registry = "public.ecr.aws/biocontainers" } process { diff --git a/tests/modules/nf-core/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config index 0a9ffca7f5f..5affc412fa4 100644 --- a/tests/modules/nf-core/vcf2maf/nextflow.config +++ b/tests/modules/nf-core/vcf2maf/nextflow.config @@ -6,7 +6,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: 'test_vcf2maf_no_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" - container = ${params.docker_url ?: 'quay.io/biocontainers'}/vcf2maf:1.6.21--hdfd78af_0 + container = ${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2maf:1.6.21--hdfd78af_0 } withName: 'test_vcf2maf_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species}" From 0799aff63927b1f99ebd5b7e3d87e72df262f18a Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 12:52:31 +0200 Subject: [PATCH 08/21] POC: One line container Co-authored-by: mahesh-panchal --- modules/nf-core/bowtie/align/main.nf | 4 +--- tests/config/nextflow.config | 3 ++- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 9557f2ab9a9..d32464d71a9 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,9 +3,7 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" } + container "${ (params.container_registry ?: 'quay.io' ) + 'mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }" input: tuple val(meta), path(reads) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 31d29fb6a7d..04f55302e31 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -3,7 +3,6 @@ params { publish_dir_mode = "copy" enable_conda = false singularity_pull_docker_container = false - docker_registry = "public.ecr.aws/biocontainers" } process { @@ -15,12 +14,14 @@ process { if ("$PROFILE" == "singularity") { singularity.enabled = true singularity.autoMounts = true + params.container_registry = 'https://depot.galaxyproject.org/singularity/' } else if ("$PROFILE" == "conda") { params.enable_conda = true } else { docker.enabled = true docker.userEmulation = true docker.runOptions = "--platform linux/x86_64" + params.container_registry = 'quay.io/biocontainers/' } // Increase time available to build Conda environment From 14a5444214d1709f9fb81a80550901d2ff174c2f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 12:58:04 +0200 Subject: [PATCH 09/21] Remove string --- modules/nf-core/bowtie/align/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index d32464d71a9..b032195f339 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,7 +3,7 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - container "${ (params.container_registry ?: 'quay.io' ) + 'mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }" + container { (params.container_registry ?: 'quay.io' ) + 'mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' } input: tuple val(meta), path(reads) From 602accbe6180992d69811f3c42680e263addf16d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 12:59:37 +0200 Subject: [PATCH 10/21] style: Space out closure --- modules/nf-core/bowtie/align/main.nf | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index b032195f339..39e6289313a 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,7 +3,10 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - container { (params.container_registry ?: 'quay.io' ) + 'mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' } + container { + (params.container_registry ?: 'quay.io' ) + + 'mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' + } input: tuple val(meta), path(reads) From 403f9715b2ee0007abd10befda45c3abb2f0f6b2 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 13:03:48 +0200 Subject: [PATCH 11/21] style: Make the image more readable --- modules/nf-core/bowtie/align/main.nf | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 39e6289313a..5ef8b370ad2 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -2,11 +2,9 @@ process BOWTIE_ALIGN { tag "$meta.id" label 'process_high' + def image = "mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - container { - (params.container_registry ?: 'quay.io' ) + - 'mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' - } + container { (params.container_registry ?: 'quay.io' ) + image } input: tuple val(meta), path(reads) From 2d6f5e817037425c843b4bee430df74606826727 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 15:13:27 +0200 Subject: [PATCH 12/21] style: Add forward slash to image name Co-authored-by: mahesh-panchal --- modules/nf-core/bowtie/align/main.nf | 4 ++-- tests/config/nextflow.config | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 5ef8b370ad2..2796c6a2c6a 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -2,9 +2,9 @@ process BOWTIE_ALIGN { tag "$meta.id" label 'process_high' - def image = "mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" + def image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - container { (params.container_registry ?: 'quay.io' ) + image } + container { (params.container_registry ?: 'quay.io/biocontainers') + image } input: tuple val(meta), path(reads) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 04f55302e31..85c7a062341 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -14,14 +14,14 @@ process { if ("$PROFILE" == "singularity") { singularity.enabled = true singularity.autoMounts = true - params.container_registry = 'https://depot.galaxyproject.org/singularity/' + params.container_registry = 'https://depot.galaxyproject.org/singularity' } else if ("$PROFILE" == "conda") { params.enable_conda = true } else { docker.enabled = true docker.userEmulation = true docker.runOptions = "--platform linux/x86_64" - params.container_registry = 'quay.io/biocontainers/' + params.container_registry = "quay.io/biocontainers" } // Increase time available to build Conda environment From a14b2cb2f5ba4359fa2b0a60395b50b2ea7e0579 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 16:27:28 +0200 Subject: [PATCH 13/21] style: Move container all together Co-authored-by: mahesh-panchal --- modules/nf-core/bowtie/align/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 2796c6a2c6a..1edc946f2f1 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,8 +3,8 @@ process BOWTIE_ALIGN { label 'process_high' def image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" + container ((params.container_registry ?: 'quay.io/biocontainers') + image) conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - container { (params.container_registry ?: 'quay.io/biocontainers') + image } input: tuple val(meta), path(reads) From 03e58e9d4b2b9a0c858d60d06264b0bb3b5be6f0 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 16:54:34 +0200 Subject: [PATCH 14/21] style: Remove container line awk -i inplace '!/workflow.containerEngine/' modules/**/**/** --- modules/nf-core/abacas/main.nf | 1 - modules/nf-core/abricate/run/main.nf | 1 - modules/nf-core/abricate/summary/main.nf | 1 - modules/nf-core/adapterremoval/main.nf | 1 - modules/nf-core/adapterremovalfixprefix/main.nf | 1 - modules/nf-core/agrvate/main.nf | 1 - modules/nf-core/allelecounter/main.nf | 1 - modules/nf-core/ampir/main.nf | 1 - modules/nf-core/amplify/predict/main.nf | 1 - modules/nf-core/amps/main.nf | 1 - modules/nf-core/amrfinderplus/run/main.nf | 1 - modules/nf-core/amrfinderplus/update/main.nf | 1 - modules/nf-core/angsd/docounts/main.nf | 1 - modules/nf-core/antismash/antismashlite/main.nf | 3 --- .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 3 --- modules/nf-core/aria2/main.nf | 1 - modules/nf-core/ariba/getref/main.nf | 1 - modules/nf-core/ariba/run/main.nf | 1 - modules/nf-core/arriba/main.nf | 1 - modules/nf-core/artic/guppyplex/main.nf | 1 - modules/nf-core/artic/minion/main.nf | 1 - modules/nf-core/ascat/main.nf | 1 - modules/nf-core/assemblyscan/main.nf | 1 - modules/nf-core/ataqv/ataqv/main.nf | 1 - modules/nf-core/ataqv/mkarv/main.nf | 1 - modules/nf-core/atlas/call/main.nf | 1 - modules/nf-core/atlas/pmd/main.nf | 1 - modules/nf-core/atlas/recal/main.nf | 1 - modules/nf-core/atlas/splitmerge/main.nf | 1 - modules/nf-core/bakta/main.nf | 1 - modules/nf-core/bamaligncleaner/main.nf | 1 - modules/nf-core/bamcmp/main.nf | 1 - modules/nf-core/bamtools/convert/main.nf | 1 - modules/nf-core/bamtools/split/main.nf | 1 - modules/nf-core/bamtools/stats/main.nf | 1 - modules/nf-core/bamutil/trimbam/main.nf | 1 - modules/nf-core/bandage/image/main.nf | 1 - modules/nf-core/bbmap/align/main.nf | 1 - modules/nf-core/bbmap/bbduk/main.nf | 1 - modules/nf-core/bbmap/bbsplit/main.nf | 1 - modules/nf-core/bbmap/clumpify/main.nf | 1 - modules/nf-core/bbmap/index/main.nf | 1 - modules/nf-core/bbmap/pileup/main.nf | 1 - modules/nf-core/bcftools/annotate/main.nf | 1 - modules/nf-core/bcftools/concat/main.nf | 1 - modules/nf-core/bcftools/consensus/main.nf | 1 - modules/nf-core/bcftools/convert/main.nf | 1 - modules/nf-core/bcftools/filter/main.nf | 1 - modules/nf-core/bcftools/index/main.nf | 1 - modules/nf-core/bcftools/isec/main.nf | 1 - modules/nf-core/bcftools/merge/main.nf | 1 - modules/nf-core/bcftools/mpileup/main.nf | 1 - modules/nf-core/bcftools/norm/main.nf | 1 - modules/nf-core/bcftools/query/main.nf | 1 - modules/nf-core/bcftools/reheader/main.nf | 1 - modules/nf-core/bcftools/roh/main.nf | 1 - modules/nf-core/bcftools/sort/main.nf | 1 - modules/nf-core/bcftools/stats/main.nf | 1 - modules/nf-core/bcftools/view/main.nf | 1 - modules/nf-core/bedtools/bamtobed/main.nf | 1 - modules/nf-core/bedtools/complement/main.nf | 1 - modules/nf-core/bedtools/genomecov/main.nf | 1 - modules/nf-core/bedtools/getfasta/main.nf | 1 - modules/nf-core/bedtools/intersect/main.nf | 1 - modules/nf-core/bedtools/makewindows/main.nf | 1 - modules/nf-core/bedtools/maskfasta/main.nf | 1 - modules/nf-core/bedtools/merge/main.nf | 1 - modules/nf-core/bedtools/slop/main.nf | 1 - modules/nf-core/bedtools/sort/main.nf | 1 - modules/nf-core/bedtools/split/main.nf | 1 - modules/nf-core/bedtools/subtract/main.nf | 1 - modules/nf-core/biobambam/bammarkduplicates2/main.nf | 1 - modules/nf-core/biobambam/bammerge/main.nf | 1 - modules/nf-core/biobambam/bamsormadup/main.nf | 1 - modules/nf-core/biscuit/align/main.nf | 1 - modules/nf-core/biscuit/biscuitblaster/main.nf | 1 - modules/nf-core/biscuit/bsconv/main.nf | 1 - modules/nf-core/biscuit/epiread/main.nf | 1 - modules/nf-core/biscuit/index/main.nf | 1 - modules/nf-core/biscuit/mergecg/main.nf | 1 - modules/nf-core/biscuit/pileup/main.nf | 1 - modules/nf-core/biscuit/qc/main.nf | 1 - modules/nf-core/biscuit/vcf2bed/main.nf | 1 - modules/nf-core/bismark/align/main.nf | 1 - modules/nf-core/bismark/deduplicate/main.nf | 1 - modules/nf-core/bismark/genomepreparation/main.nf | 1 - modules/nf-core/bismark/methylationextractor/main.nf | 1 - modules/nf-core/bismark/report/main.nf | 1 - modules/nf-core/bismark/summary/main.nf | 1 - modules/nf-core/blast/blastn/main.nf | 1 - modules/nf-core/blast/makeblastdb/main.nf | 1 - modules/nf-core/blast/tblastn/main.nf | 1 - modules/nf-core/bowtie/build/main.nf | 1 - modules/nf-core/bowtie2/align/main.nf | 1 - modules/nf-core/bowtie2/build/main.nf | 1 - modules/nf-core/bracken/bracken/main.nf | 1 - modules/nf-core/bracken/combinebrackenoutputs/main.nf | 1 - modules/nf-core/busco/main.nf | 1 - modules/nf-core/bwa/aln/main.nf | 1 - modules/nf-core/bwa/index/main.nf | 1 - modules/nf-core/bwa/mem/main.nf | 1 - modules/nf-core/bwa/sampe/main.nf | 1 - modules/nf-core/bwa/samse/main.nf | 1 - modules/nf-core/bwamem2/index/main.nf | 1 - modules/nf-core/bwamem2/mem/main.nf | 1 - modules/nf-core/bwameth/align/main.nf | 1 - modules/nf-core/bwameth/index/main.nf | 1 - modules/nf-core/cat/cat/main.nf | 1 - modules/nf-core/cat/fastq/main.nf | 1 - modules/nf-core/centrifuge/centrifuge/main.nf | 1 - modules/nf-core/centrifuge/kreport/main.nf | 1 - modules/nf-core/checkm/lineagewf/main.nf | 1 - modules/nf-core/checkm/qa/main.nf | 1 - modules/nf-core/chromap/chromap/main.nf | 1 - modules/nf-core/chromap/index/main.nf | 1 - modules/nf-core/clonalframeml/main.nf | 1 - modules/nf-core/cmseq/polymut/main.nf | 1 - modules/nf-core/cnvkit/antitarget/main.nf | 1 - modules/nf-core/cnvkit/batch/main.nf | 1 - modules/nf-core/cnvkit/reference/main.nf | 1 - modules/nf-core/cnvpytor/callcnvs/main.nf | 1 - modules/nf-core/cnvpytor/histogram/main.nf | 1 - modules/nf-core/cnvpytor/importreaddepth/main.nf | 1 - modules/nf-core/cnvpytor/partition/main.nf | 1 - modules/nf-core/cnvpytor/view/main.nf | 1 - modules/nf-core/controlfreec/assesssignificance/main.nf | 1 - modules/nf-core/controlfreec/freec/main.nf | 1 - modules/nf-core/controlfreec/freec2bed/main.nf | 1 - modules/nf-core/controlfreec/freec2circos/main.nf | 1 - modules/nf-core/controlfreec/makegraph/main.nf | 1 - modules/nf-core/cooler/cload/main.nf | 1 - modules/nf-core/cooler/digest/main.nf | 1 - modules/nf-core/cooler/dump/main.nf | 1 - modules/nf-core/cooler/merge/main.nf | 1 - modules/nf-core/cooler/zoomify/main.nf | 1 - modules/nf-core/crumble/main.nf | 1 - modules/nf-core/csvtk/concat/main.nf | 1 - modules/nf-core/csvtk/split/main.nf | 1 - modules/nf-core/custom/dumpsoftwareversions/main.nf | 1 - modules/nf-core/custom/getchromsizes/main.nf | 1 - modules/nf-core/custom/sratoolsncbisettings/main.nf | 1 - modules/nf-core/cutadapt/main.nf | 1 - modules/nf-core/damageprofiler/main.nf | 1 - modules/nf-core/dastool/dastool/main.nf | 1 - modules/nf-core/dastool/fastatocontig2bin/main.nf | 1 - modules/nf-core/dastool/scaffolds2bin/main.nf | 1 - modules/nf-core/dedup/main.nf | 1 - modules/nf-core/deeparg/downloaddata/main.nf | 2 -- modules/nf-core/deeparg/predict/main.nf | 2 -- modules/nf-core/deepbgc/download/main.nf | 1 - modules/nf-core/deepbgc/pipeline/main.nf | 1 - modules/nf-core/deeptools/bamcoverage/main.nf | 1 - modules/nf-core/deeptools/computematrix/main.nf | 1 - modules/nf-core/deeptools/plotfingerprint/main.nf | 1 - modules/nf-core/deeptools/plotheatmap/main.nf | 1 - modules/nf-core/deeptools/plotprofile/main.nf | 1 - modules/nf-core/delly/call/main.nf | 1 - modules/nf-core/diamond/blastp/main.nf | 1 - modules/nf-core/diamond/blastx/main.nf | 1 - modules/nf-core/diamond/makedb/main.nf | 1 - modules/nf-core/dragmap/align/main.nf | 1 - modules/nf-core/dragmap/hashtable/main.nf | 1 - modules/nf-core/dragonflye/main.nf | 1 - modules/nf-core/dshbio/exportsegments/main.nf | 1 - modules/nf-core/dshbio/filterbed/main.nf | 1 - modules/nf-core/dshbio/filtergff3/main.nf | 1 - modules/nf-core/dshbio/splitbed/main.nf | 1 - modules/nf-core/dshbio/splitgff3/main.nf | 1 - modules/nf-core/ectyper/main.nf | 1 - modules/nf-core/eido/convert/main.nf | 1 - modules/nf-core/eido/validate/main.nf | 1 - modules/nf-core/elprep/filter/main.nf | 1 - modules/nf-core/elprep/merge/main.nf | 1 - 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modules/nf-core/unicycler/main.nf | 1 - modules/nf-core/untar/main.nf | 1 - modules/nf-core/unzip/main.nf | 1 - modules/nf-core/vardictjava/main.nf | 1 - modules/nf-core/variantbam/main.nf | 1 - modules/nf-core/vcf2db/main.nf | 1 - modules/nf-core/vcf2maf/main.nf | 1 - modules/nf-core/vcfanno/main.nf | 1 - modules/nf-core/vcflib/vcfbreakmulti/main.nf | 1 - modules/nf-core/vcflib/vcfuniq/main.nf | 1 - modules/nf-core/vcftools/main.nf | 1 - modules/nf-core/verifybamid/verifybamid2/main.nf | 1 - modules/nf-core/vsearch/sintax/main.nf | 1 - modules/nf-core/vsearch/usearchglobal/main.nf | 1 - modules/nf-core/wgsim/main.nf | 1 - modules/nf-core/whamg/main.nf | 1 - modules/nf-core/yara/index/main.nf | 1 - modules/nf-core/yara/mapper/main.nf | 1 - 619 files changed, 625 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index 3a90b7783bf..57a43fc1a56 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -3,7 +3,6 @@ process ABACAS { label 'process_medium' conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/abacas:1.3.1--pl526_0" } diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index 843dc249b79..455cac0546d 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -3,7 +3,6 @@ process ABRICATE_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index a6097ac313f..de29132be0f 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -3,7 +3,6 @@ process ABRICATE_SUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 0427b9c4e6b..c268a9ab923 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -3,7 +3,6 @@ process ADAPTERREMOVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/adapterremoval:2.3.2--hb7ba0dd_0" } diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 45c444f6700..6498ce8a777 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -4,7 +4,6 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/adapterremovalfixprefix:0.0.5--hdfd78af_2" } diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 437eea38be0..717d6d70807 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -3,7 +3,6 @@ process AGRVATE { label 'process_low' conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/agrvate:1.0.2--hdfd78af_0" } diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index 0cc6d7735a0..f4bdfd9dc73 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -3,7 +3,6 @@ process ALLELECOUNTER { label 'process_low' conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cancerit-allelecount:4.3.0--h41abebc_0" } diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index 46da7276c94..33615924624 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -3,7 +3,6 @@ process AMPIR { label 'process_single' conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0': "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ampir:1.1.0" } diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 51fe2862403..eda1d09fffb 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -4,7 +4,6 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/amplify:1.0.3--py36hdfd78af_0" } diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 5d909a8cf54..919de50fbd4 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -2,7 +2,6 @@ process AMPS { label 'process_low' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 00730fc6277..0d4964570a8 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -3,7 +3,6 @@ process AMRFINDERPLUS_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 74a3e802249..1322384de35 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -3,7 +3,6 @@ process AMRFINDERPLUS_UPDATE { label 'process_single' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index 58b3e8a20ae..7e3e8ec2cb5 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -3,7 +3,6 @@ process ANGSD_DOCOUNTS { label 'process_low' conda (params.enable_conda ? "bioconda::angsd=0.939" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/angsd:0.939--h468462d_0" } diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 28cf3ffedce..1fb36a111a3 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -3,14 +3,11 @@ process ANTISMASH_ANTISMASHLITE { label 'process_medium' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } containerOptions { - workflow.containerEngine == 'singularity' ? "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : - workflow.containerEngine == 'docker' ? "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : '' } diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 2a3f27756cb..869f66a5c2b 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,7 +2,6 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { label 'process_single' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } @@ -13,9 +12,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { */ containerOptions { - workflow.containerEngine == 'singularity' ? "-B $database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css,$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection,$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" : - workflow.containerEngine == 'docker' ? "-v \$PWD/$database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css -v \$PWD/$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection -v \$PWD/$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" : '' } diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 12167e00380..0ad64a476f6 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -4,7 +4,6 @@ process ARIA2 { label 'process_single' conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/aria2:1.36.0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/aria2:1.36.0" } diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index abb0381bbd0..74571b2b39d 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -3,7 +3,6 @@ process ARIBA_GETREF { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': "${params.docker_registry ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 4f8d07baba3..65b15e0766b 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -3,7 +3,6 @@ process ARIBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': "${params.docker_registry ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 11c781e2998..79e0ba5a8ba 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -3,7 +3,6 @@ process ARRIBA { label 'process_medium' conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/arriba:2.3.0--haa8aa89_0" } diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 98aca407f5b..6cac7f9260d 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -3,7 +3,6 @@ process ARTIC_GUPPYPLEX { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index 524aa79d968..8d43170cb2f 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -3,7 +3,6 @@ process ARTIC_MINION { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index 46728afcb0f..e6dcb607bff 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -3,7 +3,6 @@ process ASCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" } diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index edf271bd4f7..c7698e71ebd 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -3,7 +3,6 @@ process ASSEMBLYSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/assembly-scan:0.4.1--pyhdfd78af_0" } diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index 3f5864d72c3..0fef353f2c9 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -3,7 +3,6 @@ process ATAQV_ATAQV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 75718b6ee74..550dc1d0ccb 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -2,7 +2,6 @@ process ATAQV_MKARV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 5ba4b080e89..06859c704d0 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -3,7 +3,6 @@ process ATLAS_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index 75bf97ce795..e698aa60eb5 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -3,7 +3,6 @@ process ATLAS_PMD { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index 2784b9f67c7..1ffc439108b 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -3,7 +3,6 @@ process ATLAS_RECAL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index 25f13381002..75aadf63f75 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -3,7 +3,6 @@ process ATLAS_SPLITMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index b2be31f5749..a26d3609c18 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -3,7 +3,6 @@ process BAKTA { label 'process_medium' conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bakta:1.5.0--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bakta:1.5.0--pyhdfd78af_0" } diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index ca0fb18b802..fc134bbdb2e 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -3,7 +3,6 @@ process BAMALIGNCLEANER { label 'process_low' conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bamaligncleaner:0.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 26cdf5a385a..fde6e0cec20 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -3,7 +3,6 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bamcmp:2.2--h05f6578_0" } diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index 35bf0d2bf6f..36ef012c6ce 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -3,7 +3,6 @@ process BAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index e5198942fee..c185906890e 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -3,7 +3,6 @@ process BAMTOOLS_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.2--hd03093a_0" } diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index 30fadd9cff4..d1406e4d88e 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -3,7 +3,6 @@ process BAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 1f7569b29d4..39c2c97e0d9 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -3,7 +3,6 @@ process BAMUTIL_TRIMBAM { label 'process_single' conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bamutil:1.0.15--h2e03b76_1" } diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 1292a833368..354a01e00b2 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -3,7 +3,6 @@ process BANDAGE_IMAGE { label 'process_low' conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bandage:0.8.1--hc9558a2_2" } diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 871108ff602..0ce74345577 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -3,7 +3,6 @@ process BBMAP_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index f571c95c1bb..56b0cdea79b 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -3,7 +3,6 @@ process BBMAP_BBDUK { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.90--he522d1c_1" } diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 86f77cceeda..ed9d24dc96d 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,7 +2,6 @@ process BBMAP_BBSPLIT { label 'process_high' conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.93--he522d1c_0" } diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index 185e211442f..bcb3a3349d4 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -4,7 +4,6 @@ process BBMAP_CLUMPIFY { label 'process_high_memory' conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.98--h5c4e2a8_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.98--h5c4e2a8_1" } diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index 05e1c95295c..7df52937641 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -3,7 +3,6 @@ process BBMAP_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.92--he522d1c_0" } diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 10ef64dd90e..e8cf1086449 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -3,7 +3,6 @@ process BBMAP_PILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 19f007ac8ec..86943b116b2 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_ANNOTATE { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 8003dfe556c..e651861ab90 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_CONCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index c6141e5deba..4e4f1644759 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index ac39db740a0..c80e53ea676 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_CONVERT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 6771425dfaf..3556eefa1fe 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index b1d5174374b..011187b8507 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 2d8993c72a6..328f455086a 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_ISEC { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 80e6ab7654c..a2b4fa846a2 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index 35b1761f170..9b7940fc668 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_MPILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 5aafaa4dda7..90bd84a5da9 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_NORM { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 8c9011e09ca..8ae5cfdc193 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 47dc7cb3563..888b393a113 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_REHEADER { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index a7960977493..2b9ee794538 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_ROH { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index de42b723fd4..fd0dfef7fb5 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index f40c9ac8a8c..15d00c4dbe8 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index b2ad7a3bcf5..035f192fd24 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -3,7 +3,6 @@ process BCFTOOLS_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index ec9cdc7c047..ab9975dbab9 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_BAMTOBED { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index e6dbcfbbae7..2d74cda56d3 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_COMPLEMENT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 3872a63bca5..31d2242a6fc 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 5b63ab31ac1..71f97ba62a1 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_GETFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index 0903f0290eb..27e7b28bc5e 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_INTERSECT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index 12e6b65c73e..ed7fc989fb8 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_MAKEWINDOWS { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_1" } diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index fbab190d1aa..71c3caa9e7f 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_MASKFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 1d222502b63..a1dac889df4 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index be900f7b5ca..71a5abc69a7 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_SLOP { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 676a9455eb0..13be1ada244 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_SORT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index 65487485036..1a2ce92667d 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_SPLIT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h468198e_3': "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_2" } diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index 63f1f3f8d12..13250758c76 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -3,7 +3,6 @@ process BEDTOOLS_SUBTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } diff --git a/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/modules/nf-core/biobambam/bammarkduplicates2/main.nf index 430caa92c14..2a5fb811ee5 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -3,7 +3,6 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 { label 'process_medium' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index 45b146c585a..dc96d69c391 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -3,7 +3,6 @@ process BIOBAMBAM_BAMMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1" } diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index 59df0bba89e..56f55d8893b 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -3,7 +3,6 @@ process BIOBAMBAM_BAMSORMADUP { label "process_medium" conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - container ${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1" : {params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1"} input: tuple val(meta), path(bams, stageAs: "?/*") diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index 337c20e501a..773b4770ee2 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -3,7 +3,6 @@ process BISCUIT_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index f44c872dd4a..1aa64a1160f 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -3,7 +3,6 @@ process BISCUIT_BLASTER { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index 94ae13e837c..2dc49c38594 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -3,7 +3,6 @@ process BISCUIT_BSCONV { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index 93cfcaba4c7..d0a0ca167fe 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -3,7 +3,6 @@ process BISCUIT_EPIREAD { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index a41d5a7cbf8..9ddeef912ba 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -3,7 +3,6 @@ process BISCUIT_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index 95006108419..54b68104021 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -3,7 +3,6 @@ process BISCUIT_MERGECG { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 362acbd0533..8357747cbf8 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -3,7 +3,6 @@ process BISCUIT_PILEUP { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index a17eed1db7b..04eb58e670c 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -3,7 +3,6 @@ process BISCUIT_QC { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 348b13a96b8..9372f806a4b 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -3,7 +3,6 @@ process BISCUIT_VCF2BED { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index ec9fa8b6feb..c795391f635 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -3,7 +3,6 @@ process BISMARK_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index a64a375bf1e..9db6cb43286 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -3,7 +3,6 @@ process BISMARK_DEDUPLICATE { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 2bd7d2d5fe4..174aa079c0b 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -3,7 +3,6 @@ process BISMARK_GENOMEPREPARATION { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 3bb924717f4..ef8dce3e459 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -3,7 +3,6 @@ process BISMARK_METHYLATIONEXTRACTOR { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 449041c0254..80d353c1566 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -3,7 +3,6 @@ process BISMARK_REPORT { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index ea42ad92bf9..37c2fd38bf7 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -2,7 +2,6 @@ process BISMARK_SUMMARY { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index 1bdb761d1ca..ddd45325977 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -3,7 +3,6 @@ process BLAST_BLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index a03d18706ef..977c96e6acc 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -3,7 +3,6 @@ process BLAST_MAKEBLASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 1888c50c0bf..181bd65003e 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -3,7 +3,6 @@ process BLAST_TBLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 1e51d81010e..3be7d17ceed 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -3,7 +3,6 @@ process BOWTIE_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bowtie:1.3.0--py38hed8969a_1" } diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index e28f4fd2421..35a29b94c85 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -3,7 +3,6 @@ process BOWTIE2_ALIGN { label "process_high" conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) - container { workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" } diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index a9aabb3a851..12c0b86c561 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -3,7 +3,6 @@ process BOWTIE2_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bowtie2:2.4.4--py39hbb4e92a_0" } diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index ff6bebec5ca..61a3c7d25a1 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -5,7 +5,6 @@ process BRACKEN_BRACKEN { // WARN: Version information not provided by tool on CLI. // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 41eec2a47e7..894381f84a2 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,7 +2,6 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { label 'process_low' conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 8c40cfbf261..54dbcc4aaf8 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -3,7 +3,6 @@ process BUSCO { label 'process_medium' conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/busco:5.4.3--pyhdfd78af_0" } diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 4ab817ae171..496359a63d9 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -3,7 +3,6 @@ process BWA_ALN { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa:0.7.17--h5bf99c6_8" } diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 1eab7f80231..519e789bd8b 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -3,7 +3,6 @@ process BWA_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa:0.7.17--hed695b0_7" } diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index ee2f04432a8..5aa0c156f2e 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -3,7 +3,6 @@ process BWA_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 9e0535c0836..62642f7c1b7 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -3,7 +3,6 @@ process BWA_SAMPE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 2f37920670b..1eb3c352a56 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -3,7 +3,6 @@ process BWA_SAMSE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 51b38d24ec2..b26d6047bdc 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -3,7 +3,6 @@ process BWAMEM2_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa-mem2:2.2.1--he513fc3_0" } diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index fa7f7ba9baf..56750a8415a 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -3,7 +3,6 @@ process BWAMEM2_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index c383afe98d6..efb90700a90 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -3,7 +3,6 @@ process BWAMETH_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 84f7b6b1499..c38f8ca1bb6 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -3,7 +3,6 @@ process BWAMETH_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index ab5cbc7544c..3e823497651 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -3,7 +3,6 @@ process CAT_CAT { label 'process_low' conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pigz:2.3.4" } diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index d761b319f67..550e3a95e81 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,7 +3,6 @@ process CAT_FASTQ { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 78653e0531d..37964e81d15 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -3,7 +3,6 @@ process CENTRIFUGE_CENTRIFUGE { label 'process_high' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : "${params.docker_registry ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 541c466143e..ed6c1f86056 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -3,7 +3,6 @@ process CENTRIFUGE_KREPORT { label 'process_single' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': "${params.docker_registry ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index c25ad22f71f..a7dd513fd7d 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -3,7 +3,6 @@ process CHECKM_LINEAGEWF { label 'process_medium' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index a52ce2381db..838aef4a508 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -3,7 +3,6 @@ process CHECKM_QA { label 'process_low' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index d1b3a883653..c6d2b519da1 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -3,7 +3,6 @@ process CHROMAP_CHROMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" } diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 6bd7c412ee7..8d75904c434 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -3,7 +3,6 @@ process CHROMAP_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/chromap:0.2.1--hd03093a_0" } diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 11df3d331a0..5412f2dff3e 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -3,7 +3,6 @@ process CLONALFRAMEML { label 'process_low' conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/clonalframeml:1.12--h7d875b9_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/clonalframeml:1.12--h7d875b9_1" } diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index a6325206c2b..ffc91d61423 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -4,7 +4,6 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cmseq:1.0.4--pyhb7b1952_0" } diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index a10699e15c7..48b8852d2c5 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -3,7 +3,6 @@ process CNVKIT_ANTITARGET { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 680a6d9d7c3..d762e78b9d6 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -3,7 +3,6 @@ process CNVKIT_BATCH { label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" } diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 5b656960628..57ebc046814 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -3,7 +3,6 @@ process CNVKIT_REFERENCE { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index 2f9909f4d7a..c52a66f7d73 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -3,7 +3,6 @@ process CNVPYTOR_CALLCNVS { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index a635a291cc9..25c1aaa2902 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -3,7 +3,6 @@ process CNVPYTOR_HISTOGRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index e0e611e08f7..1bf870db444 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -3,7 +3,6 @@ process CNVPYTOR_IMPORTREADDEPTH { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index d410088735e..6ce55543a90 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -3,7 +3,6 @@ process CNVPYTOR_PARTITION { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index dda48698626..9666aa3b6a1 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -3,7 +3,6 @@ process CNVPYTOR_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 4d14f15eb2f..e19c2e98af7 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -3,7 +3,6 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 7ada37c99dc..efcf73b8f8a 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -3,7 +3,6 @@ process CONTROLFREEC_FREEC { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index 83fd867418f..0aa80f9045b 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -3,7 +3,6 @@ process CONTROLFREEC_FREEC2BED { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 7a51adf7177..5b04b466ca2 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -3,7 +3,6 @@ process CONTROLFREEC_FREEC2CIRCOS { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index b2c5396d4fa..e5f07a5c40c 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -3,7 +3,6 @@ process CONTROLFREEC_MAKEGRAPH { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 04263becd20..bd2e771ec2c 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -3,7 +3,6 @@ process COOLER_CLOAD { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index d18369ef764..8810ea82422 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -3,7 +3,6 @@ process COOLER_DIGEST { label 'process_medium' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index 97d7eb1e706..f5d27af4a46 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -3,7 +3,6 @@ process COOLER_DUMP { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index cc5fe692dcd..97f6d7719f3 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -3,7 +3,6 @@ process COOLER_MERGE { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 56d18f45b07..39175e96c53 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -3,7 +3,6 @@ process COOLER_ZOOMIFY { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index be08a40306d..d430f655ac5 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -3,7 +3,6 @@ process CRUMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/crumble:0.9.0--hb0d9459_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/crumble:0.9.0--hb0d9459_1" } diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 4b484418743..62777a67a44 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -3,7 +3,6 @@ process CSVTK_CONCAT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 838a6750de6..4de09fef94f 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -3,7 +3,6 @@ process CSVTK_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index d371f29938a..41e152bbd35 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -3,7 +3,6 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index ba9b32e91a0..f64c66c0f20 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -3,7 +3,6 @@ process CUSTOM_GETCHROMSIZES { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 6e21c1a4264..4e4a36ca5c4 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -3,7 +3,6 @@ process CUSTOM_SRATOOLSNCBISETTINGS { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index e5249d5364c..0905e651b99 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -3,7 +3,6 @@ process CUTADAPT { label 'process_medium' conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/cutadapt:3.4--py39h38f01e4_1" } diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index 555393f3623..629cc3bce43 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -3,7 +3,6 @@ process DAMAGEPROFILER { label 'process_single' conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/damageprofiler:1.1--hdfd78af_2" } diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index fd36a7101ca..2890919e8b8 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -3,7 +3,6 @@ process DASTOOL_DASTOOL { label 'process_medium' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index e6fadb56440..6e1fd9031f4 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -3,7 +3,6 @@ process DASTOOL_FASTATOCONTIG2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 226360d0857..cb0818c5199 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -3,7 +3,6 @@ process DASTOOL_SCAFFOLDS2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.3--r41hdfd78af_0" } diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index be6b51b6085..87624efa83e 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -3,7 +3,6 @@ process DEDUP { label 'process_single' conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dedup:0.12.8--hdfd78af_1" } diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index 4711d6c827d..4f63de05aaf 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,14 +2,12 @@ process DEEPARG_DOWNLOADDATA { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ - containerOptions { {workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } input: diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index e019a5321cc..51c0452bc84 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -3,14 +3,12 @@ process DEEPARG_PREDICT { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ - containerOptions { {workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } input: tuple val(meta), path(fasta), val(model) diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 520a5915c28..950e606fb2e 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -2,7 +2,6 @@ process DEEPBGC_DOWNLOAD { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index c576fd3eaec..8f206e29dc2 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -3,7 +3,6 @@ process DEEPBGC_PIPELINE { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 5c8616acdbb..fe0cac8146e 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -3,7 +3,6 @@ process DEEPTOOLS_BAMCOVERAGE { label 'process_low' conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" } diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 15881f3ae18..6729a4f53f8 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -3,7 +3,6 @@ process DEEPTOOLS_COMPUTEMATRIX { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index f12a855d297..d23e3238f7e 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -3,7 +3,6 @@ process DEEPTOOLS_PLOTFINGERPRINT { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index d41a8a29620..9147dc1348b 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -3,7 +3,6 @@ process DEEPTOOLS_PLOTHEATMAP { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index 42c9e6b00fe..de098ec5384 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -3,7 +3,6 @@ process DEEPTOOLS_PLOTPROFILE { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index f47dacb590d..d61b4db5f40 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -3,7 +3,6 @@ process DELLY_CALL { label 'process_medium' conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/delly:1.1.5--h358d541_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/delly:1.1.5--h358d541_0" } diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index 03b7c321e6f..c9c3a3f459a 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -3,7 +3,6 @@ process DIAMOND_BLASTP { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 80669546d6b..68f10808136 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -3,7 +3,6 @@ process DIAMOND_BLASTX { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index 36ee64346b8..f3c3aff8e7a 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -3,7 +3,6 @@ process DIAMOND_MAKEDB { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index ee18bc73315..21c10ddc3ae 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -3,7 +3,6 @@ process DRAGMAP_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" } diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 3e6b4f9f4a7..52420b45ea3 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -3,7 +3,6 @@ process DRAGMAP_HASHTABLE { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/dragmap:1.2.1--hd4ca14e_0" } diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index 46a9df8d601..be633fb3460 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -3,7 +3,6 @@ process DRAGONFLYE { label 'process_medium' conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dragonflye:1.0.11--hdfd78af_0" } diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 4db716289cc..019f395e547 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -3,7 +3,6 @@ process DSHBIO_EXPORTSEGMENTS { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 2d59ce1eed9..566f982167d 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -3,7 +3,6 @@ process DSHBIO_FILTERBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index 79979781b51..00d862c9097 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -3,7 +3,6 @@ process DSHBIO_FILTERGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index 6e6bfc579ff..e0f2a1b0595 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -3,7 +3,6 @@ process DSHBIO_SPLITBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index da5c3fefba1..7926b0d1f46 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -3,7 +3,6 @@ process DSHBIO_SPLITGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 2fa192208f9..4b3947d4c29 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -3,7 +3,6 @@ process ECTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ectyper:1.0.0--pyhdfd78af_1" } diff --git a/modules/nf-core/eido/convert/main.nf b/modules/nf-core/eido/convert/main.nf index 8450fb34025..1bc7db167d5 100644 --- a/modules/nf-core/eido/convert/main.nf +++ b/modules/nf-core/eido/convert/main.nf @@ -3,7 +3,6 @@ process EIDO_CONVERT { label 'process_single' conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' : 'biocontainers/eido:0.1.9_cv1' }" diff --git a/modules/nf-core/eido/validate/main.nf b/modules/nf-core/eido/validate/main.nf index 9346323e51c..b6c8a40d6b8 100644 --- a/modules/nf-core/eido/validate/main.nf +++ b/modules/nf-core/eido/validate/main.nf @@ -3,7 +3,6 @@ process EIDO_VALIDATE { label 'process_single' conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' : 'biocontainers/eido:0.1.9_cv2' }" diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index e3e1ecbcd8d..51e16824055 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -3,7 +3,6 @@ process ELPREP_FILTER { label 'process_high' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index 18fb7e1f4a2..02a6cc128a7 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -3,7 +3,6 @@ process ELPREP_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 8141f56bcee..989417f356a 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -3,7 +3,6 @@ process ELPREP_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 12a2b73f954..d17456a36ca 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -3,7 +3,6 @@ process EMBOSS_SEQRET { label 'process_single' conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/emboss:6.6.0--hf657eab_5': "${params.docker_registry ?: 'quay.io/biocontainers'}/emboss:6.6.0--h440b012_4" } diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 55b9a2945a7..57868753989 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -3,7 +3,6 @@ process EMMTYPER { label 'process_low' conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/emmtyper:0.2.0--py_0" } diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 7fac544df81..25d9beb4e14 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -3,7 +3,6 @@ process ENDORSPY { label 'process_low' conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/endorspy:0.4--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/endorspy:0.4--hdfd78af_0" } diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index a0df16a9831..8f6636c0d2c 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -3,7 +3,6 @@ process ENSEMBLVEP { label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ensembl-vep:106.1--pl5321h4a94de4_0" } diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 2a1dde5dc30..804b8407681 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -3,7 +3,6 @@ process ENTREZDIRECT_ESEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index 8325bf636b3..b5a7181a2fa 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -3,7 +3,6 @@ process ENTREZDIRECT_ESUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index d70da00c417..3dcfdba12db 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -3,7 +3,6 @@ process ENTREZDIRECT_XTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index d7b78f4e4b1..fde97927ef5 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -3,7 +3,6 @@ process EPANG { label 'process_high' conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/epa-ng:0.3.8--h9a82719_1" } diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index 4dfa99a2763..c67a38728f2 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -3,7 +3,6 @@ process EXPANSIONHUNTER { label 'process_low' conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/expansionhunter:4.0.2--he785bd8_0" } diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index ebda89fd069..80ce51bb3eb 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -3,7 +3,6 @@ process FAQCS { label 'process_medium' conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/faqcs%3A2.10--r41h9a82719_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/faqcs:2.10--r41h9a82719_2" } diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index 5545d60b3cc..446b268ddf0 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -4,7 +4,6 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fargene:0.1--py27h21c881e_4" } diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index 432078d8bcf..a43d6d32b0f 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -3,7 +3,6 @@ process FASTANI { label 'process_medium' conda (params.enable_conda ? "bioconda::fastani=1.32" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fastani:1.32--he1c1bb9_0" } diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index 01163b73fc8..4b278af0406 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -3,7 +3,6 @@ process FASTAWINDOWS { label 'process_low' conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/fasta_windows:0.2.4--hec16e2b_0" } diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 32a9c49faf5..ad4fed2c60c 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -3,7 +3,6 @@ process FASTP { label 'process_medium' conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fastp:0.23.2--h79da9fb_0" } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 4cc0c20562a..8a06df12ccc 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -3,7 +3,6 @@ process FASTQC { label 'process_medium' conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fastqc:0.11.9--0" } diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index bb075099530..9a5656ecee2 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -3,7 +3,6 @@ process FASTQSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastq-scan:0.4.4--h7d875b9_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fastq-scan:0.4.4--h7d875b9_0" } diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 2f38515772c..847e05e26ac 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -2,7 +2,6 @@ process FASTTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fasttree:2.1.10--h516909a_4" } diff --git a/modules/nf-core/fcs/fcsadaptor/main.nf b/modules/nf-core/fcs/fcsadaptor/main.nf index 3f2fed41f8d..772341f0687 100644 --- a/modules/nf-core/fcs/fcsadaptor/main.nf +++ b/modules/nf-core/fcs/fcsadaptor/main.nf @@ -6,7 +6,6 @@ process FCS_FCSADAPTOR { exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers." } // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif': 'ncbi/fcs-adaptor:0.2.3' }" diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 0be640ec57a..b7b5d0bd019 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -3,7 +3,6 @@ process FFQ { label 'process_low' conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/ffq:0.2.1--pyhdfd78af_0" } diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 2eb4f59c608..90e1fa1d239 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -3,7 +3,6 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index 1f0d43b2776..bb07f634aa5 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -3,7 +3,6 @@ process FGBIO_FASTQTOBAM { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 2b7788c0f35..2310de35aa2 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -3,7 +3,6 @@ process FGBIO_GROUPREADSBYUMI { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index a1f33eea0c6..891035924c8 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -3,7 +3,6 @@ process FGBIO_SORTBAM { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 600286e1af0..fbce410a0e2 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -3,7 +3,6 @@ process FGBIO_ZIPPERBAMS { label 'process_single' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index e016c379f62..eb090c4b109 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -3,7 +3,6 @@ process FILTLONG { label 'process_low' conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/filtlong:0.2.1--h9a82719_0" } diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index 305605f2174..cb42b06fbd9 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -2,7 +2,6 @@ process FLASH { tag "$meta.id" label 'process_medium' - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/flash:1.2.11--hed695b0_5" } diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index e7ee05e3ed2..2aefc574c15 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -3,7 +3,6 @@ process FLYE { label 'process_high' conda (params.enable_conda ? "bioconda::flye=2.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/flye:2.9--py39h6935b12_1" } diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index 0d677af1753..38976a3edf6 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -3,7 +3,6 @@ process FQ_LINT { label 'process_low' conda (params.enable_conda ? "bioconda::fq=0.9.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/fq:0.9.1--h9ee0642_0" } diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 7292bc00a56..3da79f588bb 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -3,7 +3,6 @@ process FREEBAYES { label 'process_low' conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/freebayes:1.3.5--py38ha193a2f_3" } diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index b2440322f81..5d4402245dd 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -5,7 +5,6 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gamma:2.1--hdfd78af_0" } diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 7d2a81be4ee..8759887e5af 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -3,7 +3,6 @@ process GAPPA_EXAMINEASSIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 6cb7ea4c530..0332a400040 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -3,7 +3,6 @@ process GAPPA_EXAMINEGRAFT { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index d03dcf4a870..8eb9a1448e0 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -3,7 +3,6 @@ process GAPPA_EXAMINEHEATTREE { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index b6b33f8bd19..25f36811d95 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -3,7 +3,6 @@ process GATK_INDELREALIGNER { label 'process_single' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index e6b674121d9..5071514987a 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -3,7 +3,6 @@ process GATK_REALIGNERTARGETCREATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 37da825106d..34e7a3a9d1a 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -3,7 +3,6 @@ process GATK_UNIFIEDGENOTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 32182976421..8d455c8bf6e 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -3,7 +3,6 @@ process GATK4_APPLYBQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index ac121552a77..8227d07ead8 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -3,7 +3,6 @@ process GATK4_APPLYVQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 9227ffd50bf..ee9e6f5873c 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -3,7 +3,6 @@ process GATK4_BASERECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 73bbf0c9141..c08e564251f 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -3,7 +3,6 @@ process GATK4_BEDTOINTERVALLIST { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 60a1041ab4f..ce7031062d2 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -3,7 +3,6 @@ process GATK4_CALCULATECONTAMINATION { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 27a70de43ef..cafcdc34fe7 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -3,7 +3,6 @@ process GATK4_CALIBRATEDRAGSTRMODEL { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index f4a90c19cbb..96069736552 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -3,7 +3,6 @@ process GATK4_COLLECTREADCOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index fa1b29d4927..ace57318935 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -3,7 +3,6 @@ process GATK4_COLLECTSVEVIDENCE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index ab1612e75a0..fcd5d8a5215 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -3,7 +3,6 @@ process GATK4_COMBINEGVCFS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 9a6940fe7b9..52b8fcc1e7c 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -3,7 +3,6 @@ process GATK4_COMPOSESTRTABLEFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 8f8ef70cb2c..70d346c553a 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -3,7 +3,6 @@ process GATK4_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 50030dd9b8b..57774ffbf74 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -3,7 +3,6 @@ process GATK4_CREATESOMATICPANELOFNORMALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index dd34df4edda..41b27f06ee2 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -3,7 +3,6 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 630915f1dff..ddc4159e802 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -3,7 +3,6 @@ process GATK4_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 91f8567dd49..0c7ea19619e 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -3,7 +3,6 @@ process GATK4_FILTERMUTECTCALLS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 39f0bf861c6..86c1190847e 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -3,7 +3,6 @@ process GATK4_FILTERVARIANTTRANCHES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 296c51f73ee..1b0104defc8 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -3,7 +3,6 @@ process GATK4_GATHERBQSRREPORTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 57940d092c4..397526fc5e7 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -3,7 +3,6 @@ process GATK4_GATHERPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 2df87696c91..7f6926a88e1 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -3,7 +3,6 @@ process GATK4_GENOMICSDBIMPORT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index c09640c16fe..0230d6f1a45 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -3,7 +3,6 @@ process GATK4_GENOTYPEGVCFS { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 3a48ab48fb6..ac9ac8363ab 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -3,7 +3,6 @@ process GATK4_GETPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index f8383d2caca..38cf45742ff 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -3,7 +3,6 @@ process GATK4_HAPLOTYPECALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 62de34e2040..69e26207d7e 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -3,7 +3,6 @@ process GATK4_INDEXFEATUREFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index b79d113bf4e..25f7dca5a9b 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -3,7 +3,6 @@ process GATK4_INTERVALLISTTOBED { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 500b3866cb9..47b038082d7 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -3,7 +3,6 @@ process GATK4_INTERVALLISTTOOLS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 7de592eba0b..7428fc458ae 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -3,7 +3,6 @@ process GATK4_LEARNREADORIENTATIONMODEL { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 33780aa10bb..190c0faa101 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -3,7 +3,6 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 914ae80cd3d..95768df4fd7 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -3,7 +3,6 @@ process GATK4_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index cf44b267b07..4688d42fa96 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -3,7 +3,6 @@ process GATK4_MERGEBAMALIGNMENT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 56fde9e1a6a..f5f62aa568a 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -3,7 +3,6 @@ process GATK4_MERGEMUTECTSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index e968a5de638..632952c9196 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -3,7 +3,6 @@ process GATK4_MERGEVCFS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index c85dd3654ee..b1d9986cc44 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -3,7 +3,6 @@ process GATK4_MUTECT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 53f25e3d03f..18665668828 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -3,7 +3,6 @@ process GATK4_PRINTSVEVIDENCE { label 'process_single' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 04f2958f4c8..a067c7e7efc 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -3,7 +3,6 @@ process GATK4_REBLOCKGVCF { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index b01314209d3..2c35e49858c 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -3,7 +3,6 @@ process GATK4_REVERTSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index b1d0185d435..4434cb474fb 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -3,7 +3,6 @@ process GATK4_SAMTOFASTQ { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 4e3c268b967..d33fb680d79 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -3,7 +3,6 @@ process GATK4_SELECTVARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index 5cf18cc39c2..c7945569965 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -3,7 +3,6 @@ process GATK4_SPLITINTERVALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index fb89851e5b9..3240a65dad8 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -3,7 +3,6 @@ process GATK4_SPLITNCIGARREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index df864773c90..abe1fd1d32a 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -3,7 +3,6 @@ process GATK4_VARIANTFILTRATION { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 3972ca9fd82..5863b922752 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -3,7 +3,6 @@ process GATK4_VARIANTRECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index b0d44a4de30..e238f8c70b1 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -3,7 +3,6 @@ process GECCO_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gecco:0.9.2--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gecco:0.9.2--pyhdfd78af_0" } diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 9f276403ec8..3eb2dc04251 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -3,7 +3,6 @@ process GENMAP_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index d1004e644e2..7ab873339da 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -3,7 +3,6 @@ process GENMAP_MAPPABILITY { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index d1f8a1bcdbe..d7aebd25324 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -3,7 +3,6 @@ process GENMOD_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index e9bbce0c20b..ca5e2d720d7 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -3,7 +3,6 @@ process GENMOD_COMPOUND { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 13440b27065..bda7c51b7cb 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -3,7 +3,6 @@ process GENMOD_MODELS { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 56158ffe2b8..600b659dfff 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -3,7 +3,6 @@ process GENMOD_SCORE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index a126fa221f3..6a89353034c 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -3,7 +3,6 @@ process GENOMESCOPE2 { label 'process_low' conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': "${params.docker_registry ?: 'quay.io/biocontainers'}/genomescope2:2.0--py310r41hdfd78af_5" } diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index fbfc51cb0cf..7d6a9a4227d 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -3,7 +3,6 @@ process GENOTYPHI_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/genotyphi:1.9.1--hdfd78af_1" } diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 45fef7b1883..43e4f4f236a 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -3,7 +3,6 @@ process GENRICH { label 'process_high' conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/genrich:0.6.1--h5bf99c6_1" } diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index e91e0306c61..05dc2ca4d4a 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -4,7 +4,6 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gfaffix:0.1.4--hec16e2b_0" } diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 49c11e3764a..da2d54e4ea0 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -3,7 +3,6 @@ process GFFREAD { label 'process_low' conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gffread:0.12.1--h8b12597_0" } diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index 8bcd20038b9..564af1981a5 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -3,7 +3,6 @@ process GLIMPSE_CHUNK { label 'process_medium' conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/glimpse-bio:1.1.1--hce55b13_1" } diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 1dfb295cff4..b4bfd60197f 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -3,7 +3,6 @@ process GLNEXUS { label 'process_medium' conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/glnexus:1.4.1--h40d77a6_0" } diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index ad9a6cf3d67..6cda57964c4 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -3,7 +3,6 @@ process GOAT_TAXONSEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/goat:0.2.0--h92d785c_0" } diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index bb0f4ddacd2..4604a649404 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -4,7 +4,6 @@ process GRAPHMAP2_ALIGN { tag "$meta.id" conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index b2a45aa3f6e..853a028aafb 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -2,7 +2,6 @@ process GRAPHMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index d7a6a5cdfe8..ca6694f5682 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -3,7 +3,6 @@ process GSTAMA_COLLAPSE { label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 3e201cef285..780e5416f8a 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -3,7 +3,6 @@ process GSTAMA_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.2--hdfd78af_0" } diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index 3f4e36d981d..eb036c2c909 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -3,7 +3,6 @@ process GSTAMA_POLYACLEANUP { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 840310d624d..0ed6a7f2127 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -4,7 +4,6 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gtdbtk:1.5.0--pyhdfd78af_0" } diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 4aa47658c68..0d094eb19d1 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -2,7 +2,6 @@ process GUBBINS { label 'process_medium' conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gubbins:3.0.0--py39h5bf99c6_0" } diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 317e3891afd..dd68c0a7ec4 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -3,7 +3,6 @@ process GUNC_DOWNLOADDB { label 'process_single' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index e77b1ac79b6..8f8fcf4933f 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -3,7 +3,6 @@ process GUNC_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index e6768977778..698ac0f5feb 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -3,7 +3,6 @@ process GUNZIP { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index d7d2b67ea5f..e6593b5fda6 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -3,7 +3,6 @@ process GVCFTOOLS_EXTRACTVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gvcftools:0.17.0--he941832_3': "${params.docker_registry ?: 'quay.io/biocontainers'}/gvcftools:0.17.0--he941832_3" } diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 211d478db24..20d5628f5fa 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -3,7 +3,6 @@ process HAMRONIZATION_ABRICATE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index d772d3d23b2..0b345683c96 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -3,7 +3,6 @@ process HAMRONIZATION_AMRFINDERPLUS { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 4cd0c4c6138..c3dce032c41 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -3,7 +3,6 @@ process HAMRONIZATION_DEEPARG { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index f79fa50803e..8f7737a5139 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -3,7 +3,6 @@ process HAMRONIZATION_FARGENE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index 25d4ef68dfe..76c60231ec6 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -3,7 +3,6 @@ process HAMRONIZATION_RGI { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index 4a722411567..afa08189e03 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -2,7 +2,6 @@ process HAMRONIZATION_SUMMARIZE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index 47a6d44d26a..756adacc22c 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -3,7 +3,6 @@ process HAPLOCHECK { label 'process_low' conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/haplocheck:1.3.3--h4a94de4_0" } diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index f24f1c16b60..4a4579316e0 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -3,7 +3,6 @@ process HAPLOGREP2_CLASSIFY { label 'process_low' conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/haplogrep:2.4.0--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/haplogrep:2.4.0--hdfd78af_0" } diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index 03bd91fefb0..fa27c0176a3 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -4,7 +4,6 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index 6e2d69399a1..fe48445ae7d 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -4,7 +4,6 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 6561fdc16a5..e5673f25f8e 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -3,7 +3,6 @@ process HICAP { label 'process_low' conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hicap:1.0.3--py_0" } diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index 4943b42ac68..471a83f9faa 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -3,7 +3,6 @@ process HIFIASM { label 'process_high' conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hifiasm:0.15.4--h2e03b76_0" } diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 58d0923d322..1eb027eaae9 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -4,7 +4,6 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 2d02adf985e..c78cce35626 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -5,7 +5,6 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 6466c3a4960..00ffda4263b 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -4,7 +4,6 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index b02e0477a03..39d5525b02e 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -3,7 +3,6 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 4dcb7da4cf6..192afd5292a 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -4,7 +4,6 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 1bbade25e3f..0e0a85ab597 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -3,7 +3,6 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 5f4c4b5619b..70a8b66c553 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -4,7 +4,6 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index c5d86ac3874..f5463b6a9dc 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -3,7 +3,6 @@ process HMMER_ESLALIMASK { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 37e0b9413b0..00e0b0b99aa 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -3,7 +3,6 @@ process HMMER_ESLREFORMAT { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 2cfdcbb7154..43942556f7b 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -3,7 +3,6 @@ process HMMER_HMMALIGN { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index b0f5bf37db1..0f7477d0089 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -3,7 +3,6 @@ process HMMER_HMMBUILD { label 'process_low' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index f8b45a89578..1cfd229f972 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -3,7 +3,6 @@ process HMMER_HMMSEARCH { label 'process_medium' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index 0edecd14478..fdecf3d69d0 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -3,7 +3,6 @@ process HMTNOTE { label 'process_low' conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hmtnote:0.7.2--pyhdfd78af_0" } diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 18a064592e8..91f352665ff 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -4,7 +4,6 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index dda9472ae1a..280906e0150 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -4,7 +4,6 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 473a852dbbc..3868bb47253 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,7 +5,6 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" } diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 041b34405f2..71c48d94b89 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -4,7 +4,6 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index e60d7b69298..8f63cf6b1ff 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -4,7 +4,6 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 684ae576bee..241611a982d 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -4,7 +4,6 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/hpsuissero:1.0.1--hdfd78af_0" } diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index 87759bb5e59..1f7c019e57d 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -3,7 +3,6 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index c4a5817ddc8..cd15af79c07 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -4,7 +4,6 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index 0fcdbc3407f..9cbbb3554e0 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -3,7 +3,6 @@ process IDR { label 'process_low' conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/idr:2.0.4.2--py39hcbe4a3b_5" } diff --git a/modules/nf-core/imputeme/vcftoprs/main.nf b/modules/nf-core/imputeme/vcftoprs/main.nf index 4abc12bc156..fc8c6ef6c73 100644 --- a/modules/nf-core/imputeme/vcftoprs/main.nf +++ b/modules/nf-core/imputeme/vcftoprs/main.nf @@ -3,7 +3,6 @@ process IMPUTEME_VCFTOPRS { label 'process_low' conda (params.enable_conda ? "YOUR-TOOL-HERE" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img' : 'biocontainers/imputeme:vv1.0.7_cv1' }" diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index a81fcc47e99..b9ab7b8da84 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -3,7 +3,6 @@ process INSTRAIN_PROFILE { label 'process_high' conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/instrain:1.6.1--pyhdfd78af_0" } diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index 279bdeb8568..8f48a305af8 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -3,7 +3,6 @@ process IQTREE { label 'process_medium' conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/iqtree:2.1.4_beta--hdcc8f71_0" } diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index 67bd82b6fa0..eff7679a574 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -3,7 +3,6 @@ process ISMAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ismapper:2.0.2--pyhdfd78af_1" } diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index 167431990e4..522b51cb3ea 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -3,7 +3,6 @@ process ISOSEQ3_CLUSTER { label 'process_medium' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index 3db51a3a414..cd7b85d3b07 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -3,7 +3,6 @@ process ISOSEQ3_REFINE { label 'process_low' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index e84bfdde2a4..5c23137c903 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -3,7 +3,6 @@ process IVAR_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index 89ecbf4886f..4e5366e4c38 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -3,7 +3,6 @@ process IVAR_TRIM { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 0327e195261..7e249b400ee 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -3,7 +3,6 @@ process IVAR_VARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index 509321b0fa9..df247576cd1 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -8,7 +8,6 @@ process JUPYTERNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" } diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index 17bf5aab8cb..dac742bf5db 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -3,7 +3,6 @@ process KAIJU_KAIJU { label 'process_high' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index b95d6c70b74..5de61332ca8 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -3,7 +3,6 @@ process KAIJU_KAIJU2KRONA { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 83246486030..008ecbb79a4 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -3,7 +3,6 @@ process KAIJU_KAIJU2TABLE { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h2e03b76_0" } diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 4d06a2ff288..5f6fdf18946 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -3,7 +3,6 @@ process KALLISTO_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/kallisto:0.46.2--h4f7b962_1" } diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 1ba8e5090f8..cee55eb479c 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -3,7 +3,6 @@ process KALLISTOBUSTOOLS_COUNT { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 7184d05e495..e9f6057f807 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -3,7 +3,6 @@ process KALLISTOBUSTOOLS_REF { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index c7e67c83869..1475c8ced82 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -3,7 +3,6 @@ process KAT_HIST { label 'process_medium' conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/kat:2.4.2--py38hfc5f9d8_2" } diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index 8b2eaa0ada2..4ce1ff6ff12 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -3,7 +3,6 @@ process KHMER_NORMALIZEBYMEDIAN { label 'process_long' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 28b24872cae..667d8394bf0 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -3,7 +3,6 @@ process KHMER_UNIQUEKMERS { label 'process_low' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index a1e6aef5621..ae763841d89 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -3,7 +3,6 @@ process KLEBORATE { label 'process_medium' conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/kleborate:2.1.0--pyhdfd78af_1" } diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index f932b80b1a8..8f7627d361f 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -3,7 +3,6 @@ process KRAKEN2_KRAKEN2 { label 'process_high' conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" } diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index 356663493c9..63bd131c1d8 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,7 +2,6 @@ process KRAKENTOOLS_COMBINEKREPORTS { label 'process_single' conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index dd1cdfd4841..2fc8fca38c3 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -4,7 +4,6 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index ca78dc179de..dc98f4068f7 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -4,7 +4,6 @@ process KRONA_KRONADB { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 3d9c1311b02..8f29594d9cb 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -4,7 +4,6 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.8--pl5262hdfd78af_2" } diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 5d432e9942d..54a66b791ec 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -3,7 +3,6 @@ process KRONA_KTIMPORTTEXT { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.8.1--pl5321hdfd78af_1" } diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index d471c0ed537..f5426208672 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -4,7 +4,6 @@ process KRONA_KTUPDATETAXONOMY { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 5c03ea61a70..c099213edab 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -3,7 +3,6 @@ process LAST_DOTPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index b2c5cbe3a9d..1dc084500aa 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -3,7 +3,6 @@ process LAST_LASTAL { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index af991a9b316..6b6f13aa2c9 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -3,7 +3,6 @@ process LAST_LASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 00c73eacb3a..b54eb31b36f 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -3,7 +3,6 @@ process LAST_MAFCONVERT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 94950c1eea1..e1c4e480777 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -3,7 +3,6 @@ process LAST_MAFSWAP { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 9feb0863cfb..c59b54cec71 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -3,7 +3,6 @@ process LAST_POSTMASK { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index c2d0fb661a4..eedda24bca7 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -3,7 +3,6 @@ process LAST_SPLIT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index e3460b96d57..844b6865881 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -3,7 +3,6 @@ process LAST_TRAIN { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index befca1facc2..b1c11fc0bb9 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -4,7 +4,6 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/leehom:1.2.15--h29e30f7_1" } diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index 61bd31a7d00..29a8bcc476f 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -3,7 +3,6 @@ process LEGSTA { label 'process_medium' conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/legsta:0.5.1--hdfd78af_2" } diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index b8edd60b871..dc2182333eb 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -3,7 +3,6 @@ process LIMA { label 'process_low' conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/lima:2.2.0--h9ee0642_0" } diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index 72a33213d98..ba574037b7d 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -3,7 +3,6 @@ process LISSERO { label 'process_low' conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/lissero:0.4.9--py_0" } diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index 8e4a3c853e0..d6705d21d1b 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -3,7 +3,6 @@ process LOFREQ_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index f751d14b8f8..16b1cc46994 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -3,7 +3,6 @@ process LOFREQ_CALLPARALLEL { label 'process_high' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index 717bc8a9886..b4803d8d4ea 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -3,7 +3,6 @@ process LOFREQ_FILTER { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 43f1349912d..05ad799a12c 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -3,7 +3,6 @@ process LOFREQ_INDELQUAL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 17a97bd90e5..d1285d09af8 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -3,7 +3,6 @@ process MACREL_CONTIGS { label 'process_medium' conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/macrel:1.1.0--py36hc5360cc_0" } diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 93979e6057e..939210dff67 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -3,7 +3,6 @@ process MACS2_CALLPEAK { label 'process_medium' conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/macs2:2.2.7.1--py38h4a8c8d9_3" } diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 4c886768c3e..17acd241ebb 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -3,7 +3,6 @@ process MAFFT { label 'process_high' conda (params.enable_conda ? "bioconda::mafft=7.490" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mafft:7.490--h779adbc_0" } diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 37934fe95f2..2730076e36a 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -3,7 +3,6 @@ process MALT_BUILD { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/malt:0.41--1" } diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index 16d0bfb15da..e67997a212d 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -3,7 +3,6 @@ process MALT_RUN { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/malt:0.41--1" } diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index 8dec64acc80..0945300608b 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -3,7 +3,6 @@ process MALTEXTRACT { label 'process_medium' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 6c11f182c1b..43cb7ef7edd 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -3,7 +3,6 @@ process MANTA_CONVERTINVERSION { label 'process_low' conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" } diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 1ad8d0d0a31..dc418a55940 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -3,7 +3,6 @@ process MANTA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 86971230778..ca9bad682d0 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -3,7 +3,6 @@ process MANTA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 3641b443c00..9cc7c6c828c 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -3,7 +3,6 @@ process MANTA_TUMORONLY { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index 14922d998c9..319ae407a0e 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -3,7 +3,6 @@ process MAPDAMAGE2 { label 'process_single' conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mapdamage2:2.2.1--pyr40_0" } diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index f106535abe0..9c721a6ef71 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -3,7 +3,6 @@ process MASH_DIST { label 'process_low' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 7d90d249bc0..940d41b0af4 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -3,7 +3,6 @@ process MASH_SCREEN { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index ea9050e7c6e..12e07bd0769 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -2,7 +2,6 @@ process MASH_SKETCH { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index 4e5a6152f3c..740a483bbfa 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -3,7 +3,6 @@ process MASHTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mashtree:1.2.0--pl526h516909a_0" } diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 6a540f9fcc3..729988f5f7e 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -3,7 +3,6 @@ process MAXBIN2 { label 'process_medium' conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/maxbin2:2.2.7--he1b5a44_2" } diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index df9060ba5c5..884d6df3939 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -2,7 +2,6 @@ process MAXQUANT_LFQ { tag "$meta.id" label 'process_long' conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" } else { container ${params.docker_registry ?: 'quay.io/biocontainers'}/maxquant:2.0.3.0--py310hdfd78af_1 diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index d10425c645d..003bff8ecc0 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -4,7 +4,6 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mcroni:1.0.4--pyh5e36f6f_0" } diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index a9ccd61785a..c4a89fae71e 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -3,7 +3,6 @@ process MD5SUM { label 'process_single' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index 7e9e42501d7..cb8d6a463ce 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -3,7 +3,6 @@ process MEDAKA { label 'process_high' conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/medaka:1.4.4--py38h130def0_0" } diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 8e5d7512c30..1591f2b6d3b 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -3,7 +3,6 @@ process MEGAHIT { label 'process_high' conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" } diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index d39036d6f5e..aeb70eb486a 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -3,7 +3,6 @@ process MEGAN_DAA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 5dee8eb20b7..2749a414527 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -3,7 +3,6 @@ process MEGAN_RMA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index 78fa9673f2f..f350bf6a0e9 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -3,7 +3,6 @@ process MENINGOTYPE { label 'process_low' conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/meningotype:0.8.5--pyhdfd78af_0" } diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index 48eeb0424f2..305a70ee1fa 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -3,7 +3,6 @@ process MERQURY { label 'process_low' conda (params.enable_conda ? "bioconda::merqury=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/merqury:1.3--hdfd78af_1" } diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index 6d9804b9237..afa42c1e1d6 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -3,7 +3,6 @@ process MERYL_COUNT { label 'process_medium' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index a25bd71fd32..846129b94a5 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -3,7 +3,6 @@ process MERYL_HISTOGRAM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 9d6ea617072..ee06b1436ab 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -3,7 +3,6 @@ process MERYL_UNIONSUM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 7094cdd332a..f67d1894610 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -3,7 +3,6 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 3f04b8b207c..0cf8565eff1 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -3,7 +3,6 @@ process METABAT2_METABAT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 64264416674..dda987cc9e8 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,7 +2,6 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { label 'process_single' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 7eab1b61a5c..63eb904f408 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -3,7 +3,6 @@ process METAPHLAN3_METAPHLAN3 { label 'process_high' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index d6fa47d43fb..970613512c9 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -3,7 +3,6 @@ process METHYLDACKEL_EXTRACT { label 'process_medium' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index 65ff7182871..76c4c35210e 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -3,7 +3,6 @@ process METHYLDACKEL_MBIAS { label 'process_low' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 83a503c7cc0..d45f1ef16ba 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -3,7 +3,6 @@ process MINIA { label 'process_high' conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/minia:3.2.6--h9a82719_0" } diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 3eb0ebd8dca..64101a295a4 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -3,7 +3,6 @@ process MINIASM { label 'process_high' conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/miniasm:0.3_r179--h5bf99c6_2" } diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index 304da76fbea..b05e96b721e 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -3,7 +3,6 @@ process MINIMAP2_ALIGN { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" } diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 091211d13a1..d03d9fba6b4 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -2,7 +2,6 @@ process MINIMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/minimap2:2.21--h5bf99c6_0" } diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index cd3c8d99cd1..bc63c6bb7f1 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -3,7 +3,6 @@ process MLST { label 'process_low' conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mlst:2.19.0--hdfd78af_1" } diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index 312e734b2be..e94fa7431dd 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -3,7 +3,6 @@ process MOBSUITE_RECON { label 'process_medium' conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mob_suite:3.0.3--pyhdfd78af_0" } diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 39f417ac3d8..19f544cdf1b 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -3,7 +3,6 @@ process MOSDEPTH { label 'process_medium' conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mosdepth:0.3.3--hdfd78af_1"} diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index 984a8042d33..3876bb01436 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -2,7 +2,6 @@ process MOTUS_DOWNLOADDB { label 'process_low' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 545d48117d2..3394eb6284d 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -5,7 +5,6 @@ process MOTUS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index 4927264b9a8..601a8646288 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -3,7 +3,6 @@ process MOTUS_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index e033321fbb0..9a26e9651c9 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -3,7 +3,6 @@ process MSISENSOR_MSI { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index e9b5c1ea17a..f8046acadb5 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -3,7 +3,6 @@ process MSISENSOR_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index e62c4a2e212..1266251b086 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -3,7 +3,6 @@ process MSISENSOR2_MSI { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index 9e149368aed..1ad4fdaa888 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -3,7 +3,6 @@ process MSISENSOR2_SCAN { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index c19eaf3dfa9..717d4c2c6d8 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -3,7 +3,6 @@ process MSISENSORPRO_MSI_SOMATIC { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index 3e991cabf6c..b7e6a6d37dd 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -3,7 +3,6 @@ process MSISENSORPRO_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index d8e5e4f495a..9df6a9c6850 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -3,7 +3,6 @@ process MTNUCRATIO { label 'process_single' conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mtnucratio:0.7--hdfd78af_2" } diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 23aae1e73f4..468fb6531e0 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -2,7 +2,6 @@ process MULTIQC { label 'process_single' conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 1cc277874d6..715254874de 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -3,7 +3,6 @@ process MULTIVCFANALYZER { label 'process_single' conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multivcfanalyzer:0.85.2--hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/multivcfanalyzer:0.85.2--hdfd78af_1" } diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index 3eb24606be6..b2c221563fa 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -4,7 +4,6 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 64c5179f637..55ad7e55835 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -3,7 +3,6 @@ process MUSCLE { label 'process_single' conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' : "${params.docker_registry ?: 'quay.io/biocontainers'}/muscle:3.8.1551--h7d875b9_6" } diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index e8f44d9dc2a..afa2546468a 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -3,7 +3,6 @@ process MYKROBE_PREDICT { label 'process_low' conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/mykrobe:0.11.0--py39h2add14b_1" } diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index e3eb92dd45d..181bcd0e7a4 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -3,7 +3,6 @@ process NANOLYSE { label 'process_low' conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/nanolyse:1.2.0--py_0" } diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index 931eca294e9..c53a103396e 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -3,7 +3,6 @@ process NANOPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/nanoplot:1.40.0--pyhdfd78af_0" } diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index e8a8538b8d9..fc98ea35335 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -3,7 +3,6 @@ process NCBIGENOMEDOWNLOAD { label 'process_low' conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.1--pyh5e36f6f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-genome-download:0.3.1--pyh5e36f6f_0" } diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 1da1ef9ea3f..fca35a6eb15 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -3,7 +3,6 @@ process NEXTCLADE_DATASETGET { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index b38559680d4..b8bf3b367d3 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -3,7 +3,6 @@ process NEXTCLADE_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index d3439ad0e8e..b21be11c5a5 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -3,7 +3,6 @@ process NEXTGENMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextgenmap%3A0.5.5--hc9558a2_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/nextgenmap:0.5.5--hc9558a2_4" } diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index 8103d9ab7f7..a86828ae15b 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -3,7 +3,6 @@ process NGMASTER { label 'process_low' conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ngmaster:0.5.8--pyhdfd78af_1" } diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 2e92f85a93e..b5d5e42b4a0 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,7 +2,6 @@ process NGSCHECKMATE_NCM { label 'process_low' conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3': "${params.docker_registry ?: 'quay.io/biocontainers'}/ngscheckmate:1.0.0--py27r41hdfd78af_3" } diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index cbb01cd515a..243afe191f6 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -3,7 +3,6 @@ process NUCMER { label 'process_low' conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 0ae1e2ff5b7..8400c2b003f 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -3,7 +3,6 @@ process OPTITYPE { label 'process_medium' conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/optitype:1.3.5--0" } diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index f18fdff5992..080b731899e 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -3,7 +3,6 @@ process PAIRIX { label 'process_medium' conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairix:0.3.7--py36h30a8e3e_3" } diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 32497d0d1c2..498915a7ba3 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -3,7 +3,6 @@ process PAIRTOOLS_DEDUP { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index aa36c98220b..0d76cb807c7 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -3,7 +3,6 @@ process PAIRTOOLS_FLIP { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 3d3d6c217ae..8f83f7a2e17 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -3,7 +3,6 @@ process PAIRTOOLS_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 33f06b984de..466c4eda13f 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -3,7 +3,6 @@ process PAIRTOOLS_RESTRICT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index ac35659f4b1..a85b466e601 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -3,7 +3,6 @@ process PAIRTOOLS_SELECT { label 'process_medium' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index 383c8be3f94..a8ee6767203 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -3,7 +3,6 @@ process PAIRTOOLS_SORT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index 2b1db0eb0cf..fac8f2a4853 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -3,7 +3,6 @@ process PANAROO_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/panaroo:1.2.9--pyhdfd78af_0" } diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index b7724daf80a..0f1991825c1 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -3,7 +3,6 @@ process PANGOLIN { label 'process_medium' conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pangolin:4.1.1--pyhdfd78af_0" } diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index a70b25c988d..c3d31b2da76 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -4,7 +4,6 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/paraclu:10--h9a82719_1" } diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 3825912c61c..12583067881 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -3,7 +3,6 @@ process PASTY { label 'process_single' conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pasty:1.0.0--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/pasty:1.0.0--hdfd78af_0" } diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index 981037e0c60..5fcecd41d6a 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -3,7 +3,6 @@ process PBBAM_PBMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pbbam:1.7.0--h058f120_1" } diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 8e73654b88e..b8e911abc77 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -3,7 +3,6 @@ process PBCCS { label 'process_low' conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pbccs:6.2.0--h9ee0642_0" } diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 73fe4dd9e9b..7326459942d 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -3,7 +3,6 @@ process PBPTYPER { label 'process_single' conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbptyper:1.0.2--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/pbptyper:1.0.2--hdfd78af_0" } diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index c50dd521b44..429f9b0c451 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -3,7 +3,6 @@ process PEAR { label 'process_low' conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pear:0.9.6--h67092d7_8': "${params.docker_registry ?: 'quay.io/biocontainers'}/pear:0.9.6--h67092d7_8" } diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index a93a89a1421..c521bec183c 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -3,7 +3,6 @@ process PEDDY { label 'process_low' conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/peddy:0.4.8--pyh5e36f6f_0" } diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index ffedc40eccd..3f3ffc6a6e4 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -4,7 +4,6 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/phantompeakqualtools:1.2.2--0" } diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index bd6d25c3a9a..8bc27e16360 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -3,7 +3,6 @@ process PHYLOFLASH { label 'process_medium' conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/phyloflash:3.4--hdfd78af_1" } diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index dc23e2d93ab..500c7c1ef73 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -3,7 +3,6 @@ process PICARD_ADDORREPLACEREADGROUPS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index dd67a6f658a..2d35acadf52 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -3,7 +3,6 @@ process PICARD_CLEANSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index a69ea88af7b..75e766024d2 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -3,7 +3,6 @@ process PICARD_COLLECTHSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 60f6baa344c..2c11b44a889 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -3,7 +3,6 @@ process PICARD_COLLECTMULTIPLEMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index db5f7d06fc2..f79d0cb2393 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -3,7 +3,6 @@ process PICARD_COLLECTWGSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 60cbab12492..a4136418d15 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -3,7 +3,6 @@ process PICARD_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index 4d7165fcf96..6ed748786ad 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -3,7 +3,6 @@ process PICARD_CROSSCHECKFINGERPRINTS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index d8c679b3e94..e8d815b5419 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -3,7 +3,6 @@ process PICARD_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index 380b6093a47..d0dc9bb184e 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -3,7 +3,6 @@ process PICARD_FILTERSAMREADS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index 97fa949a32b..003f2c93e20 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -3,7 +3,6 @@ process PICARD_FIXMATEINFORMATION { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 9867cb5171f..9d8d6c6522b 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -3,7 +3,6 @@ process PICARD_LIFTOVERVCF { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 27810e6c4d6..c2336e87d8c 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -3,7 +3,6 @@ process PICARD_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index ad4958a9095..e168c3e8309 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -3,7 +3,6 @@ process PICARD_MERGESAMFILES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index ca3b30c979a..040f9aedb8b 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -4,7 +4,6 @@ process PICARD_RENAMESAMPLEINVCF { label 'process_single' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 4a7c888cea3..3ee512cb3f8 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -3,7 +3,6 @@ process PICARD_SORTSAM { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index eeccdf448ca..1a91a32a1f6 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -3,7 +3,6 @@ process PICARD_SORTVCF { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index b7d35925169..e3b9a71ae3d 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -3,7 +3,6 @@ process PINTS_CALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pypints:1.1.6--pyh5e36f6f_1" } diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index 67bff2c7e5b..7e7658ff32c 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -3,7 +3,6 @@ process PIRATE { label 'process_medium' conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pirate:1.0.4--hdfd78af_2" } diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index a39f0ddc33c..3523364ed26 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -4,7 +4,6 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/plasmidfinder:2.1.6--py310hdfd78af_1" } diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index 7d3cb223978..c9a10553be8 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -3,7 +3,6 @@ process PLASMIDID { label 'process_medium' conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/plasmidid:1.6.5--hdfd78af_0" } diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index 055cdda2805..7f06526bdd2 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -3,7 +3,6 @@ process PLINK_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index d4dbd78ed88..fb02426f3f9 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -3,7 +3,6 @@ process PLINK_VCF { label 'process_medium' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index e26b99b5a55..36eafd56606 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -3,7 +3,6 @@ process PLINK2_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index 1dc58e77823..447b041859f 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -3,7 +3,6 @@ process PLINK2_SCORE { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index 545842f5868..5d5f4dd90a5 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -3,7 +3,6 @@ process PLINK2_VCF { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 506780311f1..51154763c5e 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -3,7 +3,6 @@ process PMDTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pmdtools:0.60--hdfd78af_5" } diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index 40c4080f0d5..fc253f493fe 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -3,7 +3,6 @@ process PORECHOP { label 'process_medium' conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/porechop:0.2.4--py39h7cff6ad_2" } diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index a19e60f4258..07ed35c26c0 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -4,7 +4,6 @@ process PRESEQ_CCURVE { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 6706b12e784..82b07f5611c 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -4,7 +4,6 @@ process PRESEQ_LCEXTRAP { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index f7d56b026d5..df0b18914c8 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -3,7 +3,6 @@ process PRINSEQPLUSPLUS { label 'process_low' conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/prinseq-plus-plus:1.2.3--hc90279e_1" } diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index ed3f2ccd1fc..e8c9c2ebc31 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -3,7 +3,6 @@ process PRODIGAL { label 'process_single' conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" } diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 6e78b8d7ac8..afe19eb8a0e 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -3,7 +3,6 @@ process PROKKA { label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/prokka:1.14.6--pl5321hdfd78af_4" } diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index ebcc16592f8..0db53c5c5cf 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -3,7 +3,6 @@ process PYCOQC { label 'process_medium' conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pycoqc:2.5.2--py_0" } diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index 223b9211ac0..b32454034aa 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -3,7 +3,6 @@ process PYDAMAGE_ANALYZE { label 'process_medium' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index 4f75101b99b..ebb27c83804 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -3,7 +3,6 @@ process PYDAMAGE_FILTER { label 'process_single' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 40ab2bddacb..2962d843b34 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -3,7 +3,6 @@ process QCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/qcat:1.1.0--py_0" } diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 838f15045c4..9eeebdbd3d1 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -3,7 +3,6 @@ process QUALIMAP_BAMQC { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 9efbf028117..41c7906abaa 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -3,7 +3,6 @@ process QUALIMAP_BAMQCCRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" } diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 6e8f39fb857..1f17835100f 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -3,7 +3,6 @@ process QUALIMAP_RNASEQ { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index 3f16ba3eb46..a359be4d1a8 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -2,7 +2,6 @@ process QUAST { label 'process_medium' conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/quast:5.2.0--py39pl5321h2add14b_1" } diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index 79381cd2104..3979592c1f4 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -3,7 +3,6 @@ process RACON { label 'process_high' conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/racon:1.4.20--h9a82719_1" } diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index f71cb937fc5..a9e66ce6eb3 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -3,7 +3,6 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" } diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 7d3583ac824..87238e690c7 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -3,7 +3,6 @@ process RASUSA { label 'process_low' conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rasusa:0.3.0--h779adbc_1" } diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index 843c43ab952..e0adb2b6bee 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -3,7 +3,6 @@ process RAVEN { label 'process_medium' conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/raven-assembler:1.6.1--h2e03b76_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/raven-assembler:1.6.1--h2e03b76_0" } diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index 44d3909378c..fcb765e11a9 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -2,7 +2,6 @@ process RAXMLNG { label 'process_high' conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/raxml-ng:1.0.3--h32fcf60_0" } diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 9ba82b0abdc..e36a59d80a4 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -3,7 +3,6 @@ process RGI_MAIN { label 'process_medium' conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/rgi:5.2.1--pyha8f3691_2" } diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 99382e90062..8d364f03fbf 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -3,7 +3,6 @@ process RHOCALL_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/rhocall:0.5.1--py39hbf8eff0_0" } diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 9ee4dcf1e6e..f3636c768d8 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -8,7 +8,6 @@ process RMARKDOWNNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" } diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index 60c3df3bf99..0affe840d30 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -3,7 +3,6 @@ process ROARY { label 'process_medium' conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/roary:3.13.0--pl526h516909a_0" } diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 8792059dbc6..61326772ec0 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -3,7 +3,6 @@ process RSEM_CALCULATEEXPRESSION { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 1d863f103c7..8dc2c697ac2 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -3,7 +3,6 @@ process RSEM_PREPAREREFERENCE { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index ec35a4387c7..fa332ac1884 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -3,7 +3,6 @@ process RSEQC_BAMSTAT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index 3ed093da97c..de69b3dddfb 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -3,7 +3,6 @@ process RSEQC_INFEREXPERIMENT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index 873c74fa705..809ce9034a4 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -3,7 +3,6 @@ process RSEQC_INNERDISTANCE { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index d4f2db5cd92..49ab8ec9bec 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -3,7 +3,6 @@ process RSEQC_JUNCTIONANNOTATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 36c70dd3bdc..2e45b5b6d09 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -3,7 +3,6 @@ process RSEQC_JUNCTIONSATURATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index 0098e516753..db04fe63518 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -3,7 +3,6 @@ process RSEQC_READDISTRIBUTION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index d50ddd5d772..4d8120047be 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -3,7 +3,6 @@ process RSEQC_READDUPLICATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 984abbe1d3b..6cd67900546 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -3,7 +3,6 @@ process RSEQC_TIN { label 'process_high' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 6b672a53665..b180f1e19c3 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -3,7 +3,6 @@ process RTGTOOLS_PEDFILTER { label 'process_low' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index e1c6749c2d0..1e3fb3c1213 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -3,7 +3,6 @@ process RTGTOOLS_VCFEVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 2923582c45c..edeadbfcf30 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -3,7 +3,6 @@ process SALMON_INDEX { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index f7aec3c8cac..67176417d7e 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -3,7 +3,6 @@ process SALMON_QUANT { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 9e1a259d5bd..7a69f321380 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -3,7 +3,6 @@ process SAMBLASTER { label 'process_low' conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" } diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 7b461e833a6..b3f1cdb5182 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_AMPLICONCLIP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index 203762282e8..bd2c2ecce60 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_BAM2FQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 490a7deaaa6..9d5be730c11 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_COLLATE { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index b1ed5f26a79..d9117279ac6 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_COLLATEFASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index ef187b91d04..af5f1442a74 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 09498928c6b..bb6c666c4e6 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_DEPTH { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 4db56870c22..30bcbbd223c 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_DICT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index f72a6f90c58..26a0494f683 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_FAIDX { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 3e5d84ab342..57354397b2a 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_FASTA { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index a6f1b7d366d..52ed57f36b3 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_FASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 51faa31d6cb..e1d49396ad1 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_FIXMATE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b90e81decfc..9d1617c192d 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_FLAGSTAT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 6a90e259316..0390da63686 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_GETRG { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index d6321b145fa..b62822f449c 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_IDXSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 7423026fefe..baf7567447c 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index dcc05517ef0..809e1370e3e 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_MARKDUP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index d3cc2fe289b..f5d3a491831 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index dc446040945..f1014f7f5e2 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_MPILEUP { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index c3e08630920..29b530ce99c 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 885f9e337bc..4e63c4859d9 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 97798e55bd8..b589084107e 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -3,7 +3,6 @@ process SAMTOOLS_VIEW { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index 03397ce622f..a7c92341384 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -3,7 +3,6 @@ process SCOARY { label 'process_low' conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/scoary:1.6.16--py_2" } diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index fa0f653736a..c7ce7530440 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -3,7 +3,6 @@ process SCRAMBLE_CLUSTERANALYSIS { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 3c70e113e50..21fd12e4d96 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -3,7 +3,6 @@ process SCRAMBLE_CLUSTERIDENTIFIER { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index 8f0ca170369..949fb27e449 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -4,7 +4,6 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" } diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 85051e25e6d..579f2baf7ef 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -3,7 +3,6 @@ process SEQKIT_PAIR { label 'process_medium' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index 180b60a4786..e7313339efe 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -3,7 +3,6 @@ process SEQKIT_REPLACE { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index d2181270ece..7d5d4ab931a 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -3,7 +3,6 @@ process SEQKIT_SPLIT2 { label 'process_medium' conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index 646b8009535..8df0471eec3 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -3,7 +3,6 @@ process SEQKIT_STATS { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.2.0--h9ee0642_0" } diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index 860e35a553a..c244bbb70f7 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -3,7 +3,6 @@ process SEQSERO2 { label 'process_low' conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqsero2:1.2.1--py_0" } diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index a06dbf3ed15..96717581722 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -3,7 +3,6 @@ process SEQTK_MERGEPE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index 5123649b746..d30ef006dfd 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -3,7 +3,6 @@ process SEQTK_RENAME { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index b468aa6c0b5..1e1978d48cf 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -3,7 +3,6 @@ process SEQTK_SAMPLE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 8c0d2b187f7..71a2d484e49 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -3,7 +3,6 @@ process SEQTK_SEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 1f8dfcc11c9..83b923f74ce 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -3,7 +3,6 @@ process SEQTK_SUBSEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index e444ec8b5b1..e4d7a04f368 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -3,7 +3,6 @@ process SEQUENZAUTILS_BAM2SEQZ { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 0a82e63b7f6..653beff80f9 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -3,7 +3,6 @@ process SEQUENZAUTILS_GCWIGGLE { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 5b8b2b4a376..9cb2ee2b066 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -4,7 +4,6 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/seqwish:0.7.6--h5b5514e_1" } diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 1011ac61e7e..99dfd2cbe2e 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -3,7 +3,6 @@ process SEROBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/seroba:1.0.2--pyhdfd78af_1" } diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index 442b6932700..e465c125aec 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -3,7 +3,6 @@ process SEXDETERRMINE { label 'process_single' conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/sexdeterrmine:1.1.2--hdfd78af_1" } diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index f69be526e95..310a8c0dfed 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -3,7 +3,6 @@ process SHASTA { label 'process_medium' conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shasta:0.8.0--h7d875b9_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/shasta:0.8.0--h7d875b9_0" } diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index 5fcae1a8f69..f9db7b28bcd 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -3,7 +3,6 @@ process SHASUM { label 'process_low' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index b41f3d2c5fa..4464fb6608a 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -3,7 +3,6 @@ process SHIGATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/shigatyper:2.0.1--pyhdfd78af_0" } diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 858c7362f2e..55002cb4c03 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -3,7 +3,6 @@ process SHOVILL { label 'process_medium' conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/shovill:1.1.0--0" } diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 009f55b0edc..e78e6dbf309 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -3,7 +3,6 @@ process SISTR { label 'process_medium' conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/sistr_cmd:1.1.1--pyh864c0ab_2" } diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 0acfd9b019e..fdb15b73b46 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -4,7 +4,6 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/slimfastq:2.04--h87f3376_2" } diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index b25286c2d39..785b74bb76f 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -3,7 +3,6 @@ process SNAPALIGNER_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index 5aaea6bd589..45fd0ff6b08 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -3,7 +3,6 @@ process SNAPALIGNER_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index 6b090874fa2..f7b60202392 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -3,7 +3,6 @@ process SNIPPY_CORE { label 'process_medium' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_1" } diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index 49d331d6edb..9264e74be6d 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -3,7 +3,6 @@ process SNIPPY_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_2" } diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 30db8333597..f3f99d8645f 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -3,7 +3,6 @@ process SNPDISTS { label 'process_low' conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/snp-dists:0.8.2--h5bf99c6_0" } diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 6a357bcc761..9b8167afd69 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -3,7 +3,6 @@ process SNPEFF { label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/snpeff:5.1--hdfd78af_2" } diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index a034eb3e103..da90d3730d2 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -3,7 +3,6 @@ process SNPSIFT_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/snpsift:4.3.1t--hdfd78af_3" } diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index 830e7eba4d8..56c31a1745e 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -2,7 +2,6 @@ process SNPSITES { label 'process_medium' conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/snp-sites:2.5.1--hed695b0_0" } diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index ce8934cfdbe..cf650eba96f 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -4,7 +4,6 @@ process SOMALIER_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index d533f0413e2..23bbe9aa045 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -4,7 +4,6 @@ process SOMALIER_RELATE { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 729c8cc9d79..654a5bc95de 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,7 +3,6 @@ process SORTMERNA { label "process_high" conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/sortmerna:4.3.4--h9ee0642_0" } diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index 4213365ee72..b409b8183f3 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -3,7 +3,6 @@ process SOURMASH_SKETCH { label 'process_low' conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/sourmash:4.2.4--hdfd78af_0" } diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 85277cc69c9..be655bc18c8 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -3,7 +3,6 @@ process SPADES { label 'process_high' conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/spades:3.15.4--h95f258a_0" } diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index d32977bb050..222462000f9 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -3,7 +3,6 @@ process SPATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/spatyper:0.3.3--pyhdfd78af_3" } diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index cb90aa49d66..6cf4c64cce4 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -3,7 +3,6 @@ process SRATOOLS_FASTERQDUMP { label 'process_medium' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" } diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 880e192b5f2..8e50d3317d9 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -3,7 +3,6 @@ process SRATOOLS_PREFETCH { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 808ec931b0d..439b48d02a0 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -3,7 +3,6 @@ process SRST2_SRST2 { label 'process_low' conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/srst2:0.2.0--py27_2"} diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 009f790ac7f..3bfe3a035a7 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -4,7 +4,6 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/ssuissero:1.0.1--hdfd78af_0" } diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index c79f243508f..682ee58ac73 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -3,7 +3,6 @@ process STADENIOLIB_SCRAMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/staden_io_lib:1.14.14--h0d9da7e_3" } diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index adae664f69f..b2ec2a2d39b 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -3,7 +3,6 @@ process STAPHOPIASCCMEC { label 'process_low' conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/staphopia-sccmec:1.0.0--hdfd78af_0" } diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 1ee35253c97..1a4a01167a5 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,7 +3,6 @@ process STAR_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index eab9eb5ea70..217a1b70acb 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,7 +3,6 @@ process STAR_GENOMEGENERATE { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 2e7b25ec9ea..5847233ab33 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -3,7 +3,6 @@ process STRANGER { label 'process_low' conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/stranger:0.8.1--pyh5e36f6f_0" } diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 4c93da9b122..6b82116f581 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -3,7 +3,6 @@ process STRELKA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 1dbf05d39cd..c59bf194522 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -3,7 +3,6 @@ process STRELKA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 9179f064bc4..6321d973905 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -3,7 +3,6 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 22832bca83c..707d6a88586 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -3,7 +3,6 @@ process STRINGTIE_STRINGTIE { label 'process_medium' conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index c127b835841..79c67644c19 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -3,7 +3,6 @@ process SUBREAD_FEATURECOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/subread:2.0.1--hed695b0_0" } diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index bc65805dfab..300e744c683 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -2,7 +2,6 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" } diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 75658e642e0..ae5ff132541 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -3,7 +3,6 @@ process SVDB_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/svdb:2.6.1--py39h5371cbf_0" } diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index ebdb360f876..0348a561656 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -3,7 +3,6 @@ process SVTK_STANDARDIZE { label 'process_low' conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/svtk:0.0.20190615--py37h73a75cf_2" } diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 78ad2aa827f..487ad354336 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -3,7 +3,6 @@ process TABIX_BGZIP { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index ded6e9d0df3..a7fb8b38927 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -3,7 +3,6 @@ process TABIX_BGZIPTABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index fbd387731f4..8e993ac0104 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -3,7 +3,6 @@ process TABIX_TABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index a8f53f39d9d..bf1af7ffa51 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -3,7 +3,6 @@ process TAILFINDR { label 'process_high' conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" } diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index 15f53676e23..a0975ebf219 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -3,7 +3,6 @@ process TBPROFILER_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/tb-profiler:3.0.8--pypyh5e36f6f_0" } diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index adcf8c4f5e3..83c1572a426 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -3,7 +3,6 @@ process TIDDIT_COV { label 'process_low' conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/tiddit:3.0.0--py39h59fae87_1" } diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 0ad585463a5..13280e987ef 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -3,7 +3,6 @@ process TIDDIT_SV { label 'process_medium' conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/tiddit:3.1.0--py39h59fae87_1" } diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index 6d12391748c..ad638b46d93 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -3,7 +3,6 @@ process TRANSDECODER_LONGORF { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4' : 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index b647c1180a0..2a56809ee02 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -3,7 +3,6 @@ process TRANSDECODER_PREDICT { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4': 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 6afbce140bf..b13aaa10595 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -3,7 +3,6 @@ process TRIMGALORE { label 'process_high' conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/trim-galore:0.6.7--hdfd78af_0" } diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 81c15901e8f..2b8200fa43f 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -3,7 +3,6 @@ process TRIMMOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2': "${params.docker_registry ?: 'quay.io/biocontainers'}/trimmomatic:0.39--hdfd78af_2" } diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index e9c3d6fd08e..76f3c5a95de 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -4,7 +4,6 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedclip:377--h0b8a92a_2" } diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index d5c6cb763e7..040e714b863 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -4,7 +4,6 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedgraphtobigwig:377--h446ed27_1" } diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index a84ebb07c5d..301b853f1c4 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -4,7 +4,6 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--ha8a8165_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedtobigbed:377--ha8a8165_3" } diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index b6e078d6396..da6d3dd73de 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -4,7 +4,6 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" } diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index 69defb4139f..e23b84d3139 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -4,7 +4,6 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-liftover:377--h0b8a92a_3" } diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 972bcb6e795..67c8bbef6fb 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -4,7 +4,6 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-wigtobigwig:377--h0b8a92a_2" } diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index 00505e47ba0..21c523097e5 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -3,7 +3,6 @@ process ULTRA_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" } diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index e6897c4ba40..7824c685dab 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -3,7 +3,6 @@ process ULTRA_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index c1ceb5ea5b4..242d0a6462c 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -3,7 +3,6 @@ process ULTRA_PIPELINE { label 'process_high' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index d508818f1e4..f12ab9f2c2b 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -3,7 +3,6 @@ process UMITOOLS_DEDUP { label "process_medium" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 5c171b80c57..eb26f70db0e 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -3,7 +3,6 @@ process UMITOOLS_EXTRACT { label "process_low" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index c7d151ffd15..1efa6de7056 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -3,7 +3,6 @@ process UNICYCLER { label 'process_high' conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : "${params.docker_registry ?: 'quay.io/biocontainers'}/unicycler:0.4.8--py38h8162308_3" } diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index df5821cdeb1..3e018d73dfa 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -3,7 +3,6 @@ process UNTAR { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 5c7d473013a..95824c37bca 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -3,7 +3,6 @@ process UNZIP { label 'process_single' conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/p7zip:15.09--h2d50403_4" } diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index b2753e55988..2f9e9a4cbfd 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -3,7 +3,6 @@ process VARDICTJAVA { label 'process_medium' conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/vardict-java:1.8.3--hdfd78af_0" } diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 6e4ca4749ae..53684f5e319 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -4,7 +4,6 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' : "${params.docker_registry ?: 'quay.io/biocontainers'}/variantbam:1.4.4a--h7d7f7ad_5" } diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 19e081efcb2..66b3c800748 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,7 +4,6 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2db:2020.02.24--hdfd78af_1" } diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 9d4b37a8067..22150d583fc 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -5,7 +5,6 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0': "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" } diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 840bd176784..f66ba468a35 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -3,7 +3,6 @@ process VCFANNO { label 'process_low' conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/vcfanno:0.3.3--h9ee0642_0" } diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 2d2ddb12f25..0800969a609 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -3,7 +3,6 @@ process VCFLIB_VCFBREAKMULTI { label 'process_low' conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/vcflib:1.0.3--ha025227_0" } diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index f7c7f4f03b3..2da531a459a 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -4,7 +4,6 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/vcflib:1.0.3--hecb563c_1" } diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index a987d733438..83218c14c5a 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -3,7 +3,6 @@ process VCFTOOLS { label 'process_single' conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : "${params.docker_registry ?: 'quay.io/biocontainers'}/vcftools:0.1.16--he513fc3_4" } diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index fdf8d3e9b7a..736905fdbcf 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,7 +3,6 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : "${params.docker_registry ?: 'quay.io/biocontainers'}/verifybamid2:2.0.1--h19d48f6_8" } diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index f1953e98cd4..12ecfece25a 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -3,7 +3,6 @@ process VSEARCH_SINTAX { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index 857fdbf08e8..6c9ebac26db 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -3,7 +3,6 @@ process VSEARCH_USEARCHGLOBAL { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': "${params.docker_registry ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index b2f6b62fdf2..ac2be0a514e 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -3,7 +3,6 @@ process WGSIM { label 'process_medium' conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/wgsim:1.0--h5bf99c6_4': "${params.docker_registry ?: 'quay.io/biocontainers'}/wgsim:1.0--h5bf99c6_4" } diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index 104f70663b2..2f6cbd91c85 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -3,7 +3,6 @@ process WHAMG { label 'process_medium' conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1': "${params.docker_registry ?: 'quay.io/biocontainers'}/wham:1.8.0.1.2017.05.03--h8b12597_1" } diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index a4c5e7c106b..1bc11490ed4 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -3,7 +3,6 @@ process YARA_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' : "${params.docker_registry ?: 'quay.io/biocontainers'}/yara:1.0.2--2" } diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 730f8ea7da8..3f6a066ff05 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -3,7 +3,6 @@ process YARA_MAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) - container { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" } From 56e0a6972f7a198fc4376d3083cee6bd1b4275ee Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 16:56:05 +0200 Subject: [PATCH 15/21] style: Remove old logic awk -i inplace '!/quay.io\/biocontainers/' modules/**/**/** --- modules/nf-core/abacas/main.nf | 1 - modules/nf-core/abricate/run/main.nf | 1 - modules/nf-core/abricate/summary/main.nf | 1 - modules/nf-core/adapterremoval/main.nf | 1 - modules/nf-core/adapterremovalfixprefix/main.nf | 1 - modules/nf-core/agrvate/main.nf | 1 - modules/nf-core/allelecounter/main.nf | 1 - modules/nf-core/ampir/main.nf | 1 - modules/nf-core/amplify/predict/main.nf | 1 - modules/nf-core/amps/main.nf | 1 - modules/nf-core/amrfinderplus/run/main.nf | 1 - modules/nf-core/amrfinderplus/update/main.nf | 1 - modules/nf-core/angsd/docounts/main.nf | 1 - modules/nf-core/antismash/antismashlite/main.nf | 1 - modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf | 1 - modules/nf-core/aria2/main.nf | 1 - modules/nf-core/ariba/getref/main.nf | 1 - modules/nf-core/ariba/run/main.nf | 1 - modules/nf-core/arriba/main.nf | 1 - modules/nf-core/artic/guppyplex/main.nf | 1 - modules/nf-core/artic/minion/main.nf | 1 - modules/nf-core/ascat/main.nf | 1 - modules/nf-core/assemblyscan/main.nf | 1 - modules/nf-core/ataqv/ataqv/main.nf | 1 - modules/nf-core/ataqv/mkarv/main.nf | 1 - modules/nf-core/atlas/call/main.nf | 1 - modules/nf-core/atlas/pmd/main.nf | 1 - modules/nf-core/atlas/recal/main.nf | 1 - modules/nf-core/atlas/splitmerge/main.nf | 1 - modules/nf-core/bakta/main.nf | 1 - modules/nf-core/bamaligncleaner/main.nf | 1 - modules/nf-core/bamcmp/main.nf | 1 - modules/nf-core/bamtools/convert/main.nf | 1 - modules/nf-core/bamtools/split/main.nf | 1 - modules/nf-core/bamtools/stats/main.nf | 1 - modules/nf-core/bamutil/trimbam/main.nf | 1 - modules/nf-core/bandage/image/main.nf | 1 - modules/nf-core/bbmap/align/main.nf | 1 - modules/nf-core/bbmap/bbduk/main.nf | 1 - modules/nf-core/bbmap/bbsplit/main.nf | 1 - modules/nf-core/bbmap/clumpify/main.nf | 1 - modules/nf-core/bbmap/index/main.nf | 1 - modules/nf-core/bbmap/pileup/main.nf | 1 - modules/nf-core/bcftools/annotate/main.nf | 1 - modules/nf-core/bcftools/concat/main.nf | 1 - modules/nf-core/bcftools/consensus/main.nf | 1 - modules/nf-core/bcftools/convert/main.nf | 1 - modules/nf-core/bcftools/filter/main.nf | 1 - modules/nf-core/bcftools/index/main.nf | 1 - modules/nf-core/bcftools/isec/main.nf | 1 - modules/nf-core/bcftools/merge/main.nf | 1 - modules/nf-core/bcftools/mpileup/main.nf | 1 - modules/nf-core/bcftools/norm/main.nf | 1 - modules/nf-core/bcftools/query/main.nf | 1 - modules/nf-core/bcftools/reheader/main.nf | 1 - modules/nf-core/bcftools/roh/main.nf | 1 - modules/nf-core/bcftools/sort/main.nf | 1 - modules/nf-core/bcftools/stats/main.nf | 1 - modules/nf-core/bcftools/view/main.nf | 1 - modules/nf-core/bedtools/bamtobed/main.nf | 1 - modules/nf-core/bedtools/complement/main.nf | 1 - modules/nf-core/bedtools/genomecov/main.nf | 1 - modules/nf-core/bedtools/getfasta/main.nf | 1 - modules/nf-core/bedtools/intersect/main.nf | 1 - modules/nf-core/bedtools/makewindows/main.nf | 1 - modules/nf-core/bedtools/maskfasta/main.nf | 1 - modules/nf-core/bedtools/merge/main.nf | 1 - modules/nf-core/bedtools/slop/main.nf | 1 - modules/nf-core/bedtools/sort/main.nf | 1 - modules/nf-core/bedtools/split/main.nf | 1 - modules/nf-core/bedtools/subtract/main.nf | 1 - modules/nf-core/biobambam/bammerge/main.nf | 1 - modules/nf-core/biscuit/align/main.nf | 1 - modules/nf-core/biscuit/biscuitblaster/main.nf | 1 - modules/nf-core/biscuit/bsconv/main.nf | 1 - modules/nf-core/biscuit/epiread/main.nf | 1 - modules/nf-core/biscuit/index/main.nf | 1 - modules/nf-core/biscuit/mergecg/main.nf | 1 - modules/nf-core/biscuit/pileup/main.nf | 1 - modules/nf-core/biscuit/qc/main.nf | 1 - modules/nf-core/biscuit/vcf2bed/main.nf | 1 - modules/nf-core/bismark/align/main.nf | 1 - modules/nf-core/bismark/deduplicate/main.nf | 1 - modules/nf-core/bismark/genomepreparation/main.nf | 1 - modules/nf-core/bismark/methylationextractor/main.nf | 1 - modules/nf-core/bismark/report/main.nf | 1 - modules/nf-core/bismark/summary/main.nf | 1 - modules/nf-core/blast/blastn/main.nf | 1 - modules/nf-core/blast/makeblastdb/main.nf | 1 - modules/nf-core/blast/tblastn/main.nf | 1 - modules/nf-core/bowtie/align/main.nf | 1 - modules/nf-core/bowtie/build/main.nf | 1 - modules/nf-core/bowtie2/align/main.nf | 1 - modules/nf-core/bowtie2/build/main.nf | 1 - modules/nf-core/bracken/bracken/main.nf | 1 - modules/nf-core/bracken/combinebrackenoutputs/main.nf | 1 - modules/nf-core/busco/main.nf | 1 - modules/nf-core/bwa/aln/main.nf | 1 - modules/nf-core/bwa/index/main.nf | 1 - modules/nf-core/bwa/mem/main.nf | 1 - modules/nf-core/bwa/sampe/main.nf | 1 - modules/nf-core/bwa/samse/main.nf | 1 - modules/nf-core/bwamem2/index/main.nf | 1 - modules/nf-core/bwamem2/mem/main.nf | 1 - modules/nf-core/bwameth/align/main.nf | 1 - modules/nf-core/bwameth/index/main.nf | 1 - modules/nf-core/cat/cat/main.nf | 1 - modules/nf-core/centrifuge/centrifuge/main.nf | 1 - modules/nf-core/centrifuge/kreport/main.nf | 1 - modules/nf-core/checkm/lineagewf/main.nf | 1 - modules/nf-core/checkm/qa/main.nf | 1 - modules/nf-core/chromap/chromap/main.nf | 1 - modules/nf-core/chromap/index/main.nf | 1 - modules/nf-core/clonalframeml/main.nf | 1 - modules/nf-core/cmseq/polymut/main.nf | 1 - modules/nf-core/cnvkit/antitarget/main.nf | 1 - modules/nf-core/cnvkit/batch/main.nf | 1 - modules/nf-core/cnvkit/reference/main.nf | 1 - modules/nf-core/cnvpytor/callcnvs/main.nf | 1 - modules/nf-core/cnvpytor/histogram/main.nf | 1 - modules/nf-core/cnvpytor/importreaddepth/main.nf | 1 - modules/nf-core/cnvpytor/partition/main.nf | 1 - modules/nf-core/cnvpytor/view/main.nf | 1 - modules/nf-core/controlfreec/assesssignificance/main.nf | 1 - modules/nf-core/controlfreec/freec/main.nf | 1 - modules/nf-core/controlfreec/freec2bed/main.nf | 1 - modules/nf-core/controlfreec/freec2circos/main.nf | 1 - modules/nf-core/controlfreec/makegraph/main.nf | 1 - modules/nf-core/cooler/cload/main.nf | 1 - modules/nf-core/cooler/digest/main.nf | 1 - modules/nf-core/cooler/dump/main.nf | 1 - modules/nf-core/cooler/merge/main.nf | 1 - modules/nf-core/cooler/zoomify/main.nf | 1 - modules/nf-core/crumble/main.nf | 1 - modules/nf-core/csvtk/concat/main.nf | 1 - modules/nf-core/csvtk/split/main.nf | 1 - modules/nf-core/custom/dumpsoftwareversions/main.nf | 1 - modules/nf-core/custom/getchromsizes/main.nf | 1 - modules/nf-core/custom/sratoolsncbisettings/main.nf | 1 - modules/nf-core/cutadapt/main.nf | 1 - modules/nf-core/damageprofiler/main.nf | 1 - modules/nf-core/dastool/dastool/main.nf | 1 - modules/nf-core/dastool/fastatocontig2bin/main.nf | 1 - modules/nf-core/dastool/scaffolds2bin/main.nf | 1 - modules/nf-core/dedup/main.nf | 1 - modules/nf-core/deeparg/downloaddata/main.nf | 1 - modules/nf-core/deeparg/predict/main.nf | 1 - modules/nf-core/deepbgc/download/main.nf | 1 - modules/nf-core/deepbgc/pipeline/main.nf | 1 - modules/nf-core/deeptools/bamcoverage/main.nf | 1 - modules/nf-core/deeptools/computematrix/main.nf | 1 - modules/nf-core/deeptools/plotfingerprint/main.nf | 1 - modules/nf-core/deeptools/plotheatmap/main.nf | 1 - modules/nf-core/deeptools/plotprofile/main.nf | 1 - modules/nf-core/delly/call/main.nf | 1 - modules/nf-core/diamond/blastp/main.nf | 1 - modules/nf-core/diamond/blastx/main.nf | 1 - modules/nf-core/diamond/makedb/main.nf | 1 - modules/nf-core/dragmap/align/main.nf | 1 - modules/nf-core/dragmap/hashtable/main.nf | 1 - modules/nf-core/dragonflye/main.nf | 1 - modules/nf-core/dshbio/exportsegments/main.nf | 1 - modules/nf-core/dshbio/filterbed/main.nf | 1 - modules/nf-core/dshbio/filtergff3/main.nf | 1 - modules/nf-core/dshbio/splitbed/main.nf | 1 - modules/nf-core/dshbio/splitgff3/main.nf | 1 - modules/nf-core/ectyper/main.nf | 1 - modules/nf-core/elprep/filter/main.nf | 1 - modules/nf-core/elprep/merge/main.nf | 1 - modules/nf-core/elprep/split/main.nf | 1 - modules/nf-core/emboss/seqret/main.nf | 1 - modules/nf-core/emmtyper/main.nf | 1 - modules/nf-core/endorspy/main.nf | 1 - modules/nf-core/ensemblvep/main.nf | 1 - modules/nf-core/entrezdirect/esearch/main.nf | 1 - modules/nf-core/entrezdirect/esummary/main.nf | 1 - modules/nf-core/entrezdirect/xtract/main.nf | 1 - modules/nf-core/epang/main.nf | 1 - modules/nf-core/expansionhunter/main.nf | 1 - modules/nf-core/faqcs/main.nf | 1 - modules/nf-core/fargene/main.nf | 1 - modules/nf-core/fastani/main.nf | 1 - modules/nf-core/fastawindows/main.nf | 1 - modules/nf-core/fastp/main.nf | 1 - modules/nf-core/fastqc/main.nf | 1 - modules/nf-core/fastqscan/main.nf | 1 - modules/nf-core/fasttree/main.nf | 1 - modules/nf-core/ffq/main.nf | 1 - modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 1 - modules/nf-core/fgbio/fastqtobam/main.nf | 1 - modules/nf-core/fgbio/groupreadsbyumi/main.nf | 1 - modules/nf-core/fgbio/sortbam/main.nf | 1 - modules/nf-core/fgbio/zipperbams/main.nf | 1 - modules/nf-core/filtlong/main.nf | 1 - modules/nf-core/flash/main.nf | 1 - modules/nf-core/flye/main.nf | 1 - modules/nf-core/fq/lint/main.nf | 1 - modules/nf-core/freebayes/main.nf | 1 - modules/nf-core/gamma/gamma/main.nf | 1 - modules/nf-core/gappa/examineassign/main.nf | 1 - modules/nf-core/gappa/examinegraft/main.nf | 1 - modules/nf-core/gappa/examineheattree/main.nf | 1 - modules/nf-core/gatk/indelrealigner/main.nf | 1 - modules/nf-core/gatk/realignertargetcreator/main.nf | 1 - modules/nf-core/gatk/unifiedgenotyper/main.nf | 1 - modules/nf-core/gatk4/applybqsr/main.nf | 1 - modules/nf-core/gatk4/applyvqsr/main.nf | 1 - modules/nf-core/gatk4/baserecalibrator/main.nf | 1 - modules/nf-core/gatk4/bedtointervallist/main.nf | 1 - modules/nf-core/gatk4/calculatecontamination/main.nf | 1 - modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 1 - modules/nf-core/gatk4/collectreadcounts/main.nf | 1 - modules/nf-core/gatk4/collectsvevidence/main.nf | 1 - modules/nf-core/gatk4/combinegvcfs/main.nf | 1 - modules/nf-core/gatk4/composestrtablefile/main.nf | 1 - modules/nf-core/gatk4/createsequencedictionary/main.nf | 1 - modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 1 - modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 1 - modules/nf-core/gatk4/fastqtosam/main.nf | 1 - modules/nf-core/gatk4/filtermutectcalls/main.nf | 1 - modules/nf-core/gatk4/filtervarianttranches/main.nf | 1 - modules/nf-core/gatk4/gatherbqsrreports/main.nf | 1 - modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 1 - modules/nf-core/gatk4/genomicsdbimport/main.nf | 1 - modules/nf-core/gatk4/genotypegvcfs/main.nf | 1 - modules/nf-core/gatk4/getpileupsummaries/main.nf | 1 - modules/nf-core/gatk4/haplotypecaller/main.nf | 1 - modules/nf-core/gatk4/indexfeaturefile/main.nf | 1 - modules/nf-core/gatk4/intervallisttobed/main.nf | 1 - modules/nf-core/gatk4/intervallisttools/main.nf | 1 - modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 1 - modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 1 - modules/nf-core/gatk4/markduplicates/main.nf | 1 - modules/nf-core/gatk4/mergebamalignment/main.nf | 1 - modules/nf-core/gatk4/mergemutectstats/main.nf | 1 - modules/nf-core/gatk4/mergevcfs/main.nf | 1 - modules/nf-core/gatk4/mutect2/main.nf | 1 - modules/nf-core/gatk4/printsvevidence/main.nf | 1 - modules/nf-core/gatk4/reblockgvcf/main.nf | 1 - modules/nf-core/gatk4/revertsam/main.nf | 1 - modules/nf-core/gatk4/samtofastq/main.nf | 1 - modules/nf-core/gatk4/selectvariants/main.nf | 1 - modules/nf-core/gatk4/splitintervals/main.nf | 1 - modules/nf-core/gatk4/splitncigarreads/main.nf | 1 - modules/nf-core/gatk4/variantfiltration/main.nf | 1 - modules/nf-core/gatk4/variantrecalibrator/main.nf | 1 - modules/nf-core/gecco/run/main.nf | 1 - modules/nf-core/genmap/index/main.nf | 1 - modules/nf-core/genmap/mappability/main.nf | 1 - modules/nf-core/genmod/annotate/main.nf | 1 - modules/nf-core/genmod/compound/main.nf | 1 - modules/nf-core/genmod/models/main.nf | 1 - modules/nf-core/genmod/score/main.nf | 1 - modules/nf-core/genomescope2/main.nf | 1 - modules/nf-core/genotyphi/parse/main.nf | 1 - modules/nf-core/genrich/main.nf | 1 - modules/nf-core/gfaffix/main.nf | 1 - modules/nf-core/gffread/main.nf | 1 - modules/nf-core/glimpse/chunk/main.nf | 1 - modules/nf-core/glnexus/main.nf | 1 - modules/nf-core/goat/taxonsearch/main.nf | 1 - modules/nf-core/graphmap2/align/main.nf | 1 - modules/nf-core/graphmap2/index/main.nf | 1 - modules/nf-core/gstama/collapse/main.nf | 1 - modules/nf-core/gstama/merge/main.nf | 1 - modules/nf-core/gstama/polyacleanup/main.nf | 1 - modules/nf-core/gtdbtk/classifywf/main.nf | 1 - modules/nf-core/gubbins/main.nf | 1 - modules/nf-core/gunc/downloaddb/main.nf | 1 - modules/nf-core/gunc/run/main.nf | 1 - modules/nf-core/gvcftools/extractvariants/main.nf | 1 - modules/nf-core/hamronization/abricate/main.nf | 1 - modules/nf-core/hamronization/amrfinderplus/main.nf | 1 - modules/nf-core/hamronization/deeparg/main.nf | 1 - modules/nf-core/hamronization/fargene/main.nf | 1 - 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modules/nf-core/tabix/tabix/main.nf | 1 - modules/nf-core/tailfindr/main.nf | 1 - modules/nf-core/tbprofiler/profile/main.nf | 1 - modules/nf-core/tiddit/cov/main.nf | 1 - modules/nf-core/tiddit/sv/main.nf | 1 - modules/nf-core/trimgalore/main.nf | 1 - modules/nf-core/trimmomatic/main.nf | 1 - modules/nf-core/ucsc/bedclip/main.nf | 1 - modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 1 - modules/nf-core/ucsc/bedtobigbed/main.nf | 1 - modules/nf-core/ucsc/bigwigaverageoverbed/main.nf | 1 - modules/nf-core/ucsc/liftover/main.nf | 1 - modules/nf-core/ucsc/wigtobigwig/main.nf | 1 - modules/nf-core/ultra/align/main.nf | 1 - modules/nf-core/ultra/index/main.nf | 1 - modules/nf-core/ultra/pipeline/main.nf | 1 - modules/nf-core/umitools/dedup/main.nf | 1 - modules/nf-core/umitools/extract/main.nf | 1 - modules/nf-core/unicycler/main.nf | 1 - modules/nf-core/unzip/main.nf | 1 - modules/nf-core/vardictjava/main.nf | 1 - modules/nf-core/variantbam/main.nf | 1 - modules/nf-core/vcf2db/main.nf | 1 - modules/nf-core/vcf2maf/main.nf | 1 - modules/nf-core/vcfanno/main.nf | 1 - modules/nf-core/vcflib/vcfbreakmulti/main.nf | 1 - modules/nf-core/vcflib/vcfuniq/main.nf | 1 - modules/nf-core/vcftools/main.nf | 1 - modules/nf-core/verifybamid/verifybamid2/main.nf | 1 - modules/nf-core/vsearch/sintax/main.nf | 1 - modules/nf-core/vsearch/usearchglobal/main.nf | 1 - modules/nf-core/wgsim/main.nf | 1 - modules/nf-core/whamg/main.nf | 1 - modules/nf-core/yara/index/main.nf | 1 - modules/nf-core/yara/mapper/main.nf | 1 - 607 files changed, 607 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index 57a43fc1a56..4a7deb1da6d 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -4,7 +4,6 @@ process ABACAS { conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/abacas:1.3.1--pl526_0" } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index 455cac0546d..85cde9755e8 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -4,7 +4,6 @@ process ABRICATE_RUN { conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index de29132be0f..77ecfc9a912 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -4,7 +4,6 @@ process ABRICATE_SUMMARY { conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/abricate:1.0.1--ha8f3691_1" } input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index c268a9ab923..772b710800e 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -4,7 +4,6 @@ process ADAPTERREMOVAL { conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/adapterremoval:2.3.2--hb7ba0dd_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 6498ce8a777..533655571a3 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -5,7 +5,6 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) 'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/adapterremovalfixprefix:0.0.5--hdfd78af_2" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 717d6d70807..221121a68d9 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -4,7 +4,6 @@ process AGRVATE { conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/agrvate:1.0.2--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index f4bdfd9dc73..b73b32d57be 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -4,7 +4,6 @@ process ALLELECOUNTER { conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) 'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cancerit-allelecount:4.3.0--h41abebc_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index 33615924624..6c2b1827ef6 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -4,7 +4,6 @@ process AMPIR { conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) 'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ampir:1.1.0" } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index eda1d09fffb..2b46c278d3e 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -5,7 +5,6 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) 'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/amplify:1.0.3--py36hdfd78af_0" } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 919de50fbd4..d4c39be16be 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -3,7 +3,6 @@ process AMPS { conda (params.enable_conda ? "bioconda::hops=0.35" : null) 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 0d4964570a8..a4777d9822c 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -4,7 +4,6 @@ process AMRFINDERPLUS_RUN { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 1322384de35..25997648646 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -4,7 +4,6 @@ process AMRFINDERPLUS_UPDATE { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-amrfinderplus:3.10.30--h6e70893_0" } output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index 7e3e8ec2cb5..adb0eab4d1d 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -4,7 +4,6 @@ process ANGSD_DOCOUNTS { conda (params.enable_conda ? "bioconda::angsd=0.939" : null) 'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/angsd:0.939--h468462d_0" } input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 1fb36a111a3..02c66e21f9f 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -4,7 +4,6 @@ process ANTISMASH_ANTISMASHLITE { conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } containerOptions { "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 869f66a5c2b..59e636abb1c 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -3,7 +3,6 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/antismash-lite:6.0.1--pyhdfd78af_1" } /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 0ad64a476f6..8ea20398021 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -5,7 +5,6 @@ process ARIA2 { conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) 'https://depot.galaxyproject.org/singularity/aria2:1.36.0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/aria2:1.36.0" } input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index 74571b2b39d..e8aeb799403 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -4,7 +4,6 @@ process ARIBA_GETREF { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 65b15e0766b..aee87de1351 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -4,7 +4,6 @@ process ARIBA_RUN { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ariba:2.14.6--py39h67e14b5_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 79e0ba5a8ba..01f87748e2a 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -4,7 +4,6 @@ process ARRIBA { conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/arriba:2.3.0--haa8aa89_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 6cac7f9260d..4834bc8385f 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -4,7 +4,6 @@ process ARTIC_GUPPYPLEX { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index 8d43170cb2f..e7ae81aeb9b 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -4,7 +4,6 @@ process ARTIC_MINION { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/artic:1.2.2--pyhdfd78af_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index e6dcb607bff..e0e1c260e70 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -4,7 +4,6 @@ process ASCAT { conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" } input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index c7698e71ebd..af269b84daf 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -4,7 +4,6 @@ process ASSEMBLYSCAN { conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) 'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/assembly-scan:0.4.1--pyhdfd78af_0" } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index 0fef353f2c9..5141e66540c 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -4,7 +4,6 @@ process ATAQV_ATAQV { conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } input: tuple val(meta), path(bam), path(bai), path(peak_file) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 550dc1d0ccb..cf5d99fd833 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -3,7 +3,6 @@ process ATAQV_MKARV { conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ataqv:1.3.0--py39hccc85d7_2" } input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 06859c704d0..66b1b80e0b2 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -4,7 +4,6 @@ process ATLAS_CALL { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index e698aa60eb5..6621acf0ec1 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -4,7 +4,6 @@ process ATLAS_PMD { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index 1ffc439108b..879354024d8 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -4,7 +4,6 @@ process ATLAS_RECAL { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index 75aadf63f75..41ee8a2dff7 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -4,7 +4,6 @@ process ATLAS_SPLITMERGE { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/atlas:0.9.9--h082e891_0" } input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index a26d3609c18..51836d6031b 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -4,7 +4,6 @@ process BAKTA { conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) 'https://depot.galaxyproject.org/singularity/bakta:1.5.0--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bakta:1.5.0--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index fc134bbdb2e..b3bf855d85e 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -4,7 +4,6 @@ process BAMALIGNCLEANER { conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) 'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bamaligncleaner:0.2.1--pyhdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index fde6e0cec20..32b9638375c 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -4,7 +4,6 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) 'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bamcmp:2.2--h05f6578_0" } input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index 36ef012c6ce..49c0f00b972 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -4,7 +4,6 @@ process BAMTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index c185906890e..b1b1845f608 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -4,7 +4,6 @@ process BAMTOOLS_SPLIT { conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.2--hd03093a_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index d1406e4d88e..75e5940cc46 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -4,7 +4,6 @@ process BAMTOOLS_STATS { conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bamtools:2.5.1--h9a82719_9" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 39c2c97e0d9..01013e3364b 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -4,7 +4,6 @@ process BAMUTIL_TRIMBAM { conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) 'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bamutil:1.0.15--h2e03b76_1" } input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 354a01e00b2..9fb57b6bb11 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -4,7 +4,6 @@ process BANDAGE_IMAGE { conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bandage:0.8.1--hc9558a2_2" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 0ce74345577..f4cb69a1fd8 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -4,7 +4,6 @@ process BBMAP_ALIGN { conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 56b0cdea79b..bdf4c2443ba 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -4,7 +4,6 @@ process BBMAP_BBDUK { conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.90--he522d1c_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index ed9d24dc96d..1bc2d081ac7 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -3,7 +3,6 @@ process BBMAP_BBSPLIT { conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) 'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.93--he522d1c_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index bcb3a3349d4..c2a9829a166 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -5,7 +5,6 @@ process BBMAP_CLUMPIFY { conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) 'https://depot.galaxyproject.org/singularity/bbmap:38.98--h5c4e2a8_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.98--h5c4e2a8_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index 7df52937641..7cae94a11d9 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -4,7 +4,6 @@ process BBMAP_INDEX { conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) 'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bbmap:38.92--he522d1c_0" } input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index e8cf1086449..07093a634fe 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -4,7 +4,6 @@ process BBMAP_PILEUP { conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 86943b116b2..4f714d4db3a 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_ANNOTATE { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index e651861ab90..b2c732ea32e 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_CONCAT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index 4e4f1644759..9460ab6b283 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_CONSENSUS { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index c80e53ea676..f75273e8f92 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 3556eefa1fe..37190046388 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_FILTER { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 011187b8507..e675e2966f6 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_INDEX { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 328f455086a..70064f578a5 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_ISEC { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index a2b4fa846a2..8fdaf50afcf 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_MERGE { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index 9b7940fc668..e464b92675b 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_MPILEUP { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 90bd84a5da9..56945f7c729 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_NORM { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 8ae5cfdc193..6881140e7fc 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_QUERY { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 888b393a113..b5749321521 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_REHEADER { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 2b9ee794538..2b391adf4dc 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_ROH { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index fd0dfef7fb5..9fe0c3507af 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_SORT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 15d00c4dbe8..10944af6b80 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_STATS { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 035f192fd24..5f7af0bab37 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -4,7 +4,6 @@ process BCFTOOLS_VIEW { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bcftools:1.15.1--h0ea216a_0" } input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index ab9975dbab9..ed7c6ad1e3a 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_BAMTOBED { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index 2d74cda56d3..f3c5546a3ca 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_COMPLEMENT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 31d2242a6fc..049a400f0b5 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_GENOMECOV { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 71f97ba62a1..d6ab655e192 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_GETFASTA { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: path bed diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index 27e7b28bc5e..377adae1dd9 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_INTERSECT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index ed7fc989fb8..e010e6b40c7 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_MAKEWINDOWS { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_1" } input: tuple val(meta), path(regions) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index 71c3caa9e7f..d1ccaceb743 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_MASKFASTA { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index a1dac889df4..56004810e70 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_MERGE { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index 71a5abc69a7..ccc52a12e4b 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_SLOP { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 13be1ada244..485afd600fd 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_SORT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index 1a2ce92667d..a5da2f9fe9e 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_SPLIT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h468198e_3': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--h7d7f7ad_2" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index 13250758c76..e2386a1c2b6 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -4,7 +4,6 @@ process BEDTOOLS_SUBTRACT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bedtools:2.30.0--hc088bd4_0" } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index dc96d69c391..5f6c56fc806 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -4,7 +4,6 @@ process BIOBAMBAM_BAMMERGE { conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/biobambam:2.0.183--h9f5acd7_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index 773b4770ee2..bb161586aea 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -4,7 +4,6 @@ process BISCUIT_ALIGN { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 1aa64a1160f..19626f248f6 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -4,7 +4,6 @@ process BISCUIT_BLASTER { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index 2dc49c38594..f8bc0bb4660 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -4,7 +4,6 @@ process BISCUIT_BSCONV { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index d0a0ca167fe..9649d4999db 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -4,7 +4,6 @@ process BISCUIT_EPIREAD { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(bam), path(bai), path(snp_bed) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 9ddeef912ba..0402f19b26e 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -4,7 +4,6 @@ process BISCUIT_INDEX { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index 54b68104021..1407a6ec802 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -4,7 +4,6 @@ process BISCUIT_MERGECG { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 8357747cbf8..1a21a43f11f 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -4,7 +4,6 @@ process BISCUIT_PILEUP { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index 04eb58e670c..962ff532b55 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -4,7 +4,6 @@ process BISCUIT_QC { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/biscuit:1.0.2.20220113--h81a5ba2_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 9372f806a4b..49c87e499f4 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -4,7 +4,6 @@ process BISCUIT_VCF2BED { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index c795391f635..76a817190ca 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -4,7 +4,6 @@ process BISMARK_ALIGN { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index 9db6cb43286..00eecc00a52 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -4,7 +4,6 @@ process BISMARK_DEDUPLICATE { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 174aa079c0b..88de080e969 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -4,7 +4,6 @@ process BISMARK_GENOMEPREPARATION { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index ef8dce3e459..fbc597274a5 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -4,7 +4,6 @@ process BISMARK_METHYLATIONEXTRACTOR { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 80d353c1566..6790ea38b69 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -4,7 +4,6 @@ process BISMARK_REPORT { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 37c2fd38bf7..4acf142c197 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -3,7 +3,6 @@ process BISMARK_SUMMARY { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bismark:0.23.0--0" } input: path(bam) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index ddd45325977..a51f3017599 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -4,7 +4,6 @@ process BLAST_BLASTN { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 977c96e6acc..03f8293ba0d 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -4,7 +4,6 @@ process BLAST_MAKEBLASTDB { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 181bd65003e..4e19447602f 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -4,7 +4,6 @@ process BLAST_TBLASTN { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/blast:2.12.0--pl5262h3289130_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 1edc946f2f1..46f2ee9039c 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,7 +3,6 @@ process BOWTIE_ALIGN { label 'process_high' def image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" - container ((params.container_registry ?: 'quay.io/biocontainers') + image) conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) input: diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 3be7d17ceed..2000e64fcf7 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -4,7 +4,6 @@ process BOWTIE_BUILD { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bowtie:1.3.0--py38hed8969a_1" } input: path fasta diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 35a29b94c85..fa8d2d202d9 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -4,7 +4,6 @@ process BOWTIE2_ALIGN { conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 12c0b86c561..53ce8e48408 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -4,7 +4,6 @@ process BOWTIE2_BUILD { conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bowtie2:2.4.4--py39hbb4e92a_0" } input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index 61a3c7d25a1..c696f517e07 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -6,7 +6,6 @@ process BRACKEN_BRACKEN { // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } input: tuple val(meta), path(kraken_report) diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 894381f84a2..228f3d47761 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -3,7 +3,6 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { conda (params.enable_conda ? "bioconda::bracken=2.7" : null) 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/bracken:2.7--py39hc16433a_0" } input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 54dbcc4aaf8..85410fdd549 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -4,7 +4,6 @@ process BUSCO { conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) 'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/busco:5.4.3--pyhdfd78af_0" } input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 496359a63d9..2c4fcddc7ca 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -4,7 +4,6 @@ process BWA_ALN { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa:0.7.17--h5bf99c6_8" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 519e789bd8b..3e927523661 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -4,7 +4,6 @@ process BWA_INDEX { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa:0.7.17--hed695b0_7" } input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 5aa0c156f2e..31397c3cea8 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -4,7 +4,6 @@ process BWA_MEM { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 62642f7c1b7..b22324ec152 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -4,7 +4,6 @@ process BWA_SAMPE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 1eb3c352a56..0f4e486ca98 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -4,7 +4,6 @@ process BWA_SAMSE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index b26d6047bdc..37d62e96f1d 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -4,7 +4,6 @@ process BWAMEM2_INDEX { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bwa-mem2:2.2.1--he513fc3_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 56750a8415a..3a9cd9683ca 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -4,7 +4,6 @@ process BWAMEM2_MEM { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index efb90700a90..c1313007b66 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -4,7 +4,6 @@ process BWAMETH_ALIGN { conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index c38f8ca1bb6..85b73b821e0 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -4,7 +4,6 @@ process BWAMETH_INDEX { conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/bwameth:0.2.2--py_1" } input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 3e823497651..0bf0994b7b1 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -4,7 +4,6 @@ process CAT_CAT { conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pigz:2.3.4" } input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 37964e81d15..3eeb54d3241 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -4,7 +4,6 @@ process CENTRIFUGE_CENTRIFUGE { conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index ed6c1f86056..50525f26d1b 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -4,7 +4,6 @@ process CENTRIFUGE_KREPORT { conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': - "${params.docker_registry ?: 'quay.io/biocontainers'}/centrifuge:1.0.4_beta--h9a82719_6" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index a7dd513fd7d..ea5e13bfd0d 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -4,7 +4,6 @@ process CHECKM_LINEAGEWF { conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 838aef4a508..ee357a639a0 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -4,7 +4,6 @@ process CHECKM_QA { conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/checkm-genome:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index c6d2b519da1..edfa903189b 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -4,7 +4,6 @@ process CHROMAP_CHROMAP { conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 8d75904c434..ab3907f8edf 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -4,7 +4,6 @@ process CHROMAP_INDEX { conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/chromap:0.2.1--hd03093a_0" } input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 5412f2dff3e..edd2a24db61 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -4,7 +4,6 @@ process CLONALFRAMEML { conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) 'https://depot.galaxyproject.org/singularity/clonalframeml:1.12--h7d875b9_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/clonalframeml:1.12--h7d875b9_1" } input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index ffc91d61423..fd90e526ab2 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -5,7 +5,6 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) 'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cmseq:1.0.4--pyhb7b1952_0" } input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index 48b8852d2c5..400c8d7656d 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -4,7 +4,6 @@ process CNVKIT_ANTITARGET { conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index d762e78b9d6..49a1c58dc67 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -4,7 +4,6 @@ process CNVKIT_BATCH { conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" } input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 57ebc046814..cf3fe10f9f9 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -4,7 +4,6 @@ process CNVKIT_REFERENCE { conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvkit:0.9.9--pyhdfd78af_0" } input: path fasta diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index c52a66f7d73..d17bc030dd4 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -4,7 +4,6 @@ process CNVPYTOR_CALLCNVS { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 25c1aaa2902..053c05a7ee5 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -4,7 +4,6 @@ process CNVPYTOR_HISTOGRAM { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index 1bf870db444..bdb89da30d6 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -4,7 +4,6 @@ process CNVPYTOR_IMPORTREADDEPTH { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(input_file), path(index) diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index 6ce55543a90..9f548c7dd54 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -4,7 +4,6 @@ process CNVPYTOR_PARTITION { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index 9666aa3b6a1..e6ed0eb4694 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -4,7 +4,6 @@ process CNVPYTOR_VIEW { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/cnvpytor:1.2.1--pyhdfd78af_0" } input: tuple val(meta), path(pytor_files) diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index e19c2e98af7..04800233e7c 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -4,7 +4,6 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index efcf73b8f8a..33c1e6009d6 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -4,7 +4,6 @@ process CONTROLFREEC_FREEC { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index 0aa80f9045b..6efbe1ca315 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -4,7 +4,6 @@ process CONTROLFREEC_FREEC2BED { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 5b04b466ca2..b00a24d3561 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -4,7 +4,6 @@ process CONTROLFREEC_FREEC2CIRCOS { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index e5f07a5c40c..23498141697 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -4,7 +4,6 @@ process CONTROLFREEC_MAKEGRAPH { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/control-freec:11.6--h1b792b2_1" } input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index bd2e771ec2c..2b3632e6580 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -4,7 +4,6 @@ process COOLER_CLOAD { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(pairs), path(index) diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index 8810ea82422..b4e21a61cd6 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -4,7 +4,6 @@ process COOLER_DIGEST { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: path fasta diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index f5d27af4a46..ee9563db147 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -4,7 +4,6 @@ process COOLER_DUMP { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index 97f6d7719f3..5be4eb9061b 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -4,7 +4,6 @@ process COOLER_MERGE { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 39175e96c53..830e27c2ac7 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -4,7 +4,6 @@ process COOLER_ZOOMIFY { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cooler:0.8.11--pyh3252c3a_0" } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index d430f655ac5..7d6d78fb6ec 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -4,7 +4,6 @@ process CRUMBLE { conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) 'https://depot.galaxyproject.org/singularity/crumble:0.9.0--hb0d9459_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/crumble:0.9.0--hb0d9459_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 62777a67a44..81d7a0d0336 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -4,7 +4,6 @@ process CSVTK_CONCAT { conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 4de09fef94f..6f6028514df 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -4,7 +4,6 @@ process CSVTK_SPLIT { conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/csvtk:0.23.0--h9ee0642_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 41e152bbd35..cb4cd830552 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,7 +4,6 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index f64c66c0f20..121686f400c 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -4,7 +4,6 @@ process CUSTOM_GETCHROMSIZES { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 4e4a36ca5c4..14f35d4f02d 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -4,7 +4,6 @@ process CUSTOM_SRATOOLSNCBISETTINGS { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } output: path('*.mkfg') , emit: ncbi_settings diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 0905e651b99..405e98a6650 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -4,7 +4,6 @@ process CUTADAPT { conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/cutadapt:3.4--py39h38f01e4_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index 629cc3bce43..fe2a0dee638 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -4,7 +4,6 @@ process DAMAGEPROFILER { conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) 'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/damageprofiler:1.1--hdfd78af_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index 2890919e8b8..fe366727317 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -4,7 +4,6 @@ process DASTOOL_DASTOOL { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index 6e1fd9031f4..e04464e705d 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -4,7 +4,6 @@ process DASTOOL_FASTATOCONTIG2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.4--r41hdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index cb0818c5199..5e04e70e265 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -4,7 +4,6 @@ process DASTOOL_SCAFFOLDS2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) 'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/das_tool:1.1.3--r41hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index 87624efa83e..3740ffb883c 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -4,7 +4,6 @@ process DEDUP { conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) 'https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dedup:0.12.8--hdfd78af_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index 4f63de05aaf..b02f7388c7f 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -3,7 +3,6 @@ process DEEPARG_DOWNLOADDATA { conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 51c0452bc84..dfd6f333944 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -4,7 +4,6 @@ process DEEPARG_PREDICT { conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/deeparg:1.0.2--pyhdfd78af_1" } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 950e606fb2e..0dc2a71ed1f 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -3,7 +3,6 @@ process DEEPBGC_DOWNLOAD { conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index 8f206e29dc2..a1e150059a2 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -4,7 +4,6 @@ process DEEPBGC_PIPELINE { conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/deepbgc:0.1.30--pyhb7b1952_1" } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index fe0cac8146e..c256d28bff9 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -4,7 +4,6 @@ process DEEPTOOLS_BAMCOVERAGE { conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 6729a4f53f8..45d65d2484b 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -4,7 +4,6 @@ process DEEPTOOLS_COMPUTEMATRIX { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index d23e3238f7e..1982a599388 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -4,7 +4,6 @@ process DEEPTOOLS_PLOTFINGERPRINT { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index 9147dc1348b..ed50b7b5e2a 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -4,7 +4,6 @@ process DEEPTOOLS_PLOTHEATMAP { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index de098ec5384..d31ab9f71cd 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -4,7 +4,6 @@ process DEEPTOOLS_PLOTPROFILE { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/deeptools:3.5.1--py_0" } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index d61b4db5f40..0ddfdfdc09d 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -4,7 +4,6 @@ process DELLY_CALL { conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) 'https://depot.galaxyproject.org/singularity/delly:1.1.5--h358d541_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/delly:1.1.5--h358d541_0" } input: tuple val(meta), path(input), path(input_index), path(exclude_bed) diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index c9c3a3f459a..a0a725148b0 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -4,7 +4,6 @@ process DIAMOND_BLASTP { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 68f10808136..4e5159bd3ef 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -4,7 +4,6 @@ process DIAMOND_BLASTX { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index f3c3aff8e7a..9cfed59c06f 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -4,7 +4,6 @@ process DIAMOND_MAKEDB { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/diamond:2.0.15--hb97b32f_0" } input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index 21c10ddc3ae..a76735ffcb7 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -4,7 +4,6 @@ process DRAGMAP_ALIGN { conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 52420b45ea3..b364e8d43d7 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -4,7 +4,6 @@ process DRAGMAP_HASHTABLE { conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/dragmap:1.2.1--hd4ca14e_0" } input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index be633fb3460..fbfe1c62db0 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -4,7 +4,6 @@ process DRAGONFLYE { conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) 'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dragonflye:1.0.11--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 019f395e547..ec060abbd58 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -4,7 +4,6 @@ process DSHBIO_EXPORTSEGMENTS { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 566f982167d..3299b66a9fc 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -4,7 +4,6 @@ process DSHBIO_FILTERBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index 00d862c9097..c3d46b2725a 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -4,7 +4,6 @@ process DSHBIO_FILTERGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index e0f2a1b0595..bae090ae854 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -4,7 +4,6 @@ process DSHBIO_SPLITBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 7926b0d1f46..09959398983 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -4,7 +4,6 @@ process DSHBIO_SPLITGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/dsh-bio:2.1--hdfd78af_0" } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 4b3947d4c29..0b57919758b 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -4,7 +4,6 @@ process ECTYPER { conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ectyper:1.0.0--pyhdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 51e16824055..9573b30af0e 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -4,7 +4,6 @@ process ELPREP_FILTER { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index 02a6cc128a7..1fcd11a9330 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -4,7 +4,6 @@ process ELPREP_MERGE { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 989417f356a..3465a68d741 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -4,7 +4,6 @@ process ELPREP_SPLIT { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/elprep:5.1.2--he881be0_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index d17456a36ca..c9dabd6b20d 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -4,7 +4,6 @@ process EMBOSS_SEQRET { conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) 'https://depot.galaxyproject.org/singularity/emboss:6.6.0--hf657eab_5': - "${params.docker_registry ?: 'quay.io/biocontainers'}/emboss:6.6.0--h440b012_4" } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 57868753989..3ea8545a173 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -4,7 +4,6 @@ process EMMTYPER { conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) 'https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/emmtyper:0.2.0--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 25d9beb4e14..a783b1dc8b3 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -4,7 +4,6 @@ process ENDORSPY { conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) 'https://depot.galaxyproject.org/singularity/endorspy:0.4--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/endorspy:0.4--hdfd78af_0" } input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index 8f6636c0d2c..c45873f64d6 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -4,7 +4,6 @@ process ENSEMBLVEP { conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ensembl-vep:106.1--pl5321h4a94de4_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 804b8407681..0a3e77d55c1 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -4,7 +4,6 @@ process ENTREZDIRECT_ESEARCH { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), val(term) diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index b5a7181a2fa..4127e977c30 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -4,7 +4,6 @@ process ENTREZDIRECT_ESUMMARY { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), val(uid), path(uids_file) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index 3dcfdba12db..0384254d5e7 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -4,7 +4,6 @@ process ENTREZDIRECT_XTRACT { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/entrez-direct:16.2--he881be0_1" } input: tuple val(meta), path(xml_input) diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index fde97927ef5..c365088c8a9 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -4,7 +4,6 @@ process EPANG { conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/epa-ng:0.3.8--h9a82719_1" } input: tuple val(meta), path(queryaln) diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index c67a38728f2..73620c85e12 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -4,7 +4,6 @@ process EXPANSIONHUNTER { conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) 'https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/expansionhunter:4.0.2--he785bd8_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index 80ce51bb3eb..ee3456e60b8 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -4,7 +4,6 @@ process FAQCS { conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) 'https://depot.galaxyproject.org/singularity/faqcs%3A2.10--r41h9a82719_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/faqcs:2.10--r41h9a82719_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index 446b268ddf0..179ea874d9c 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -5,7 +5,6 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fargene:0.1--py27h21c881e_4" } input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index a43d6d32b0f..c72611d2cae 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -4,7 +4,6 @@ process FASTANI { conda (params.enable_conda ? "bioconda::fastani=1.32" : null) 'https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fastani:1.32--he1c1bb9_0" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index 4b278af0406..b7e1aac576c 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -4,7 +4,6 @@ process FASTAWINDOWS { conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) 'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/fasta_windows:0.2.4--hec16e2b_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index ad4fed2c60c..60b5dac75d9 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -4,7 +4,6 @@ process FASTP { conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fastp:0.23.2--h79da9fb_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 8a06df12ccc..8b9f6616f57 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -4,7 +4,6 @@ process FASTQC { conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fastqc:0.11.9--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index 9a5656ecee2..53545ca5a06 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -4,7 +4,6 @@ process FASTQSCAN { conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) 'https://depot.galaxyproject.org/singularity/fastq-scan:0.4.4--h7d875b9_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fastq-scan:0.4.4--h7d875b9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 847e05e26ac..66ff760a339 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -3,7 +3,6 @@ process FASTTREE { conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) 'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fasttree:2.1.10--h516909a_4" } input: path alignment diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index b7b5d0bd019..6187e889758 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -4,7 +4,6 @@ process FFQ { conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) 'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ffq:0.2.1--pyhdfd78af_0" } input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 90e1fa1d239..fbb1a3f1807 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -4,7 +4,6 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index bb07f634aa5..c3a9ed7ac03 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -4,7 +4,6 @@ process FGBIO_FASTQTOBAM { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 2310de35aa2..ac30aa8bfd3 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -4,7 +4,6 @@ process FGBIO_GROUPREADSBYUMI { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(taggedbam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index 891035924c8..61fc7c25495 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -4,7 +4,6 @@ process FGBIO_SORTBAM { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index fbce410a0e2..ba3fb6dfb21 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -4,7 +4,6 @@ process FGBIO_ZIPPERBAMS { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/fgbio:2.0.2--hdfd78af_0" } input: tuple val(meta), path(unmapped_bam) diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index eb090c4b109..95cc86f3d66 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -4,7 +4,6 @@ process FILTLONG { conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/filtlong:0.2.1--h9a82719_0" } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index cb42b06fbd9..11fcf6f472d 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -3,7 +3,6 @@ process FLASH { label 'process_medium' 'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/flash:1.2.11--hed695b0_5" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 2aefc574c15..c773757f8c1 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -4,7 +4,6 @@ process FLYE { conda (params.enable_conda ? "bioconda::flye=2.9" : null) 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/flye:2.9--py39h6935b12_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index 38976a3edf6..f7516dadf4d 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -4,7 +4,6 @@ process FQ_LINT { conda (params.enable_conda ? "bioconda::fq=0.9.1" : null) 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/fq:0.9.1--h9ee0642_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 3da79f588bb..406c0c37b4a 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -4,7 +4,6 @@ process FREEBAYES { conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) 'https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/freebayes:1.3.5--py38ha193a2f_3" } input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 5d4402245dd..5e1869603ad 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -6,7 +6,6 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) 'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gamma:2.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 8759887e5af..ad675a4b057 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -4,7 +4,6 @@ process GAPPA_EXAMINEASSIGN { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 0332a400040..6a63e115ae1 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -4,7 +4,6 @@ process GAPPA_EXAMINEGRAFT { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 8eb9a1448e0..5c709401dd2 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -4,7 +4,6 @@ process GAPPA_EXAMINEHEATTREE { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gappa:0.8.0--h9a82719_0" } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 25f36811d95..36dff0d20a9 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -4,7 +4,6 @@ process GATK_INDELREALIGNER { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index 5071514987a..400746be8e2 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -4,7 +4,6 @@ process GATK_REALIGNERTARGETCREATOR { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 34e7a3a9d1a..82ce641c57c 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -4,7 +4,6 @@ process GATK_UNIFIEDGENOTYPER { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk:3.5--hdfd78af_11" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 8d455c8bf6e..ae4e189080d 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,7 +4,6 @@ process GATK4_APPLYBQSR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 8227d07ead8..21c1b43c855 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -4,7 +4,6 @@ process GATK4_APPLYVQSR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index ee9e6f5873c..e0cd109ed65 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,7 +4,6 @@ process GATK4_BASERECALIBRATOR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index c08e564251f..3c553a6a387 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,7 +4,6 @@ process GATK4_BEDTOINTERVALLIST { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index ce7031062d2..737d295033d 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,7 +4,6 @@ process GATK4_CALCULATECONTAMINATION { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index cafcdc34fe7..b09c91f8ca4 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,7 +4,6 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 96069736552..6bb2c62f2fa 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -4,7 +4,6 @@ process GATK4_COLLECTREADCOUNTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index ace57318935..19beae65b6c 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -4,7 +4,6 @@ process GATK4_COLLECTSVEVIDENCE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index fcd5d8a5215..10cb3e27afe 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,7 +4,6 @@ process GATK4_COMBINEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 52b8fcc1e7c..a45f8e0c16a 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,7 +4,6 @@ process GATK4_COMPOSESTRTABLEFILE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 70d346c553a..1d7096b2a35 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,7 +4,6 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 57774ffbf74..704f2df1cf5 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -4,7 +4,6 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 41b27f06ee2..9e0fca3fde4 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -4,7 +4,6 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index ddc4159e802..58c0b776bb9 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -4,7 +4,6 @@ process GATK4_FASTQTOSAM { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 0c7ea19619e..7bad97d53a9 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -4,7 +4,6 @@ process GATK4_FILTERMUTECTCALLS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 86c1190847e..6bc7c1bac14 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,7 +4,6 @@ process GATK4_FILTERVARIANTTRANCHES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 1b0104defc8..6236c110d12 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -4,7 +4,6 @@ process GATK4_GATHERBQSRREPORTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 397526fc5e7..a402f06e078 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,7 +4,6 @@ process GATK4_GATHERPILEUPSUMMARIES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 7f6926a88e1..f6651004df1 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,7 +4,6 @@ process GATK4_GENOMICSDBIMPORT { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 0230d6f1a45..d0140d51977 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,7 +4,6 @@ process GATK4_GENOTYPEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index ac9ac8363ab..18535b7b79f 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,7 +4,6 @@ process GATK4_GETPILEUPSUMMARIES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 38cf45742ff..956e0399512 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,7 +4,6 @@ process GATK4_HAPLOTYPECALLER { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 69e26207d7e..4e7699851d4 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,7 +4,6 @@ process GATK4_INDEXFEATUREFILE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 25f7dca5a9b..72db1e0cd8a 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,7 +4,6 @@ process GATK4_INTERVALLISTTOBED { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 47b038082d7..b9b70dd6815 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,7 +4,6 @@ process GATK4_INTERVALLISTTOOLS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 7428fc458ae..8d617a97ec4 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,7 +4,6 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 190c0faa101..9cbd4906629 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -4,7 +4,6 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 95768df4fd7..371856afc8c 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -4,7 +4,6 @@ process GATK4_MARKDUPLICATES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 4688d42fa96..8db32b45196 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -4,7 +4,6 @@ process GATK4_MERGEBAMALIGNMENT { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index f5f62aa568a..f06a0fe0fde 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,7 +4,6 @@ process GATK4_MERGEMUTECTSTATS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 632952c9196..0a4bf92b038 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -4,7 +4,6 @@ process GATK4_MERGEVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index b1d9986cc44..dfdf62bd39d 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -4,7 +4,6 @@ process GATK4_MUTECT2 { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 18665668828..8cdc06996be 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -4,7 +4,6 @@ process GATK4_PRINTSVEVIDENCE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index a067c7e7efc..395a5e2ec9b 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -4,7 +4,6 @@ process GATK4_REBLOCKGVCF { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 2c35e49858c..39a95272f4b 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -4,7 +4,6 @@ process GATK4_REVERTSAM { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 4434cb474fb..f7ebf57bdf0 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -4,7 +4,6 @@ process GATK4_SAMTOFASTQ { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index d33fb680d79..7f234828af1 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -4,7 +4,6 @@ process GATK4_SELECTVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index c7945569965..be6091e08a0 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -4,7 +4,6 @@ process GATK4_SPLITINTERVALS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 3240a65dad8..230973d87eb 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -4,7 +4,6 @@ process GATK4_SPLITNCIGARREADS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index abe1fd1d32a..01684cf0940 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -4,7 +4,6 @@ process GATK4_VARIANTFILTRATION { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 5863b922752..b660abae359 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,7 +4,6 @@ process GATK4_VARIANTRECALIBRATOR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gatk4:4.2.6.1--hdfd78af_0" } input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index e238f8c70b1..c10e98d6321 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -4,7 +4,6 @@ process GECCO_RUN { conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) 'https://depot.galaxyproject.org/singularity/gecco:0.9.2--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gecco:0.9.2--pyhdfd78af_0" } input: tuple val(meta), path(input), path(hmm) diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 3eb2dc04251..ab22cb798e7 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -4,7 +4,6 @@ process GENMAP_INDEX { conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index 7ab873339da..9ebd1663cc0 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -4,7 +4,6 @@ process GENMAP_MAPPABILITY { conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/genmap:1.3.0--h1b792b2_1" } input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index d7aebd25324..37b1af4a7eb 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -4,7 +4,6 @@ process GENMOD_ANNOTATE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index ca5e2d720d7..881b4e53b5a 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -4,7 +4,6 @@ process GENMOD_COMPOUND { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index bda7c51b7cb..96cb4c5517e 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -4,7 +4,6 @@ process GENMOD_MODELS { conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 600b659dfff..e376d2d82ba 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -4,7 +4,6 @@ process GENMOD_SCORE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/genmod:3.7.4--pyh5e36f6f_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index 6a89353034c..e55747a2e59 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -4,7 +4,6 @@ process GENOMESCOPE2 { conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': - "${params.docker_registry ?: 'quay.io/biocontainers'}/genomescope2:2.0--py310r41hdfd78af_5" } input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index 7d6a9a4227d..c57cde1dd45 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -4,7 +4,6 @@ process GENOTYPHI_PARSE { conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) 'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/genotyphi:1.9.1--hdfd78af_1" } input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 43e4f4f236a..274b3474e3f 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -4,7 +4,6 @@ process GENRICH { conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/genrich:0.6.1--h5bf99c6_1" } input: tuple val(meta), path(treatment_bam) diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index 05dc2ca4d4a..d1b21640899 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -5,7 +5,6 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) 'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gfaffix:0.1.4--hec16e2b_0" } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index da2d54e4ea0..2c459b68724 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -4,7 +4,6 @@ process GFFREAD { conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gffread:0.12.1--h8b12597_0" } input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index 564af1981a5..110efddc399 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -4,7 +4,6 @@ process GLIMPSE_CHUNK { conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/glimpse-bio:1.1.1--hce55b13_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index b4bfd60197f..2480c1fde69 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -4,7 +4,6 @@ process GLNEXUS { conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/glnexus:1.4.1--h40d77a6_0" } input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index 6cda57964c4..777606f4793 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -4,7 +4,6 @@ process GOAT_TAXONSEARCH { conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) 'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/goat:0.2.0--h92d785c_0" } input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index 4604a649404..c2f9de78e0c 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -5,7 +5,6 @@ process GRAPHMAP2_ALIGN { conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index 853a028aafb..f6c329c7ec1 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -3,7 +3,6 @@ process GRAPHMAP2_INDEX { conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/graphmap:0.6.3--he513fc3_0" } input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index ca6694f5682..6845650c5cf 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -4,7 +4,6 @@ process GSTAMA_COLLAPSE { conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 780e5416f8a..26885f82b02 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -4,7 +4,6 @@ process GSTAMA_MERGE { conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.2--hdfd78af_0" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index eb036c2c909..a34a1561345 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -4,7 +4,6 @@ process GSTAMA_POLYACLEANUP { conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gs-tama:1.0.3--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 0ed6a7f2127..0ae59ebb639 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -5,7 +5,6 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gtdbtk:1.5.0--pyhdfd78af_0" } input: tuple val(meta), path("bins/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 0d094eb19d1..197df72a0b6 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -3,7 +3,6 @@ process GUBBINS { conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gubbins:3.0.0--py39h5bf99c6_0" } input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index dd68c0a7ec4..0d242f56565 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -4,7 +4,6 @@ process GUNC_DOWNLOADDB { conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index 8f8fcf4933f..3906c0fe047 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -4,7 +4,6 @@ process GUNC_RUN { conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/gunc:1.0.5--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index e6593b5fda6..f9545489d96 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -4,7 +4,6 @@ process GVCFTOOLS_EXTRACTVARIANTS { conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) 'https://depot.galaxyproject.org/singularity/gvcftools:0.17.0--he941832_3': - "${params.docker_registry ?: 'quay.io/biocontainers'}/gvcftools:0.17.0--he941832_3" } input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 20d5628f5fa..2d514e05d61 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -4,7 +4,6 @@ process HAMRONIZATION_ABRICATE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index 0b345683c96..90317f9140c 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -4,7 +4,6 @@ process HAMRONIZATION_AMRFINDERPLUS { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index c3dce032c41..2609f20a01d 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -4,7 +4,6 @@ process HAMRONIZATION_DEEPARG { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index 8f7737a5139..e0fdb675093 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -4,7 +4,6 @@ process HAMRONIZATION_FARGENE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index 76c60231ec6..010a47e15b0 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -4,7 +4,6 @@ process HAMRONIZATION_RGI { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index afa08189e03..a25837f1a03 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -3,7 +3,6 @@ process HAMRONIZATION_SUMMARIZE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hamronization:1.1.1--pyhdfd78af_0" } input: path(reports) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index 756adacc22c..d472319259c 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -4,7 +4,6 @@ process HAPLOCHECK { conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/haplocheck:1.3.3--h4a94de4_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 4a4579316e0..5b114b08179 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -4,7 +4,6 @@ process HAPLOGREP2_CLASSIFY { conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) 'https://depot.galaxyproject.org/singularity/haplogrep:2.4.0--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/haplogrep:2.4.0--hdfd78af_0" } input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index fa27c0176a3..d546611f776 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -5,7 +5,6 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index fe48445ae7d..06324578e03 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -5,7 +5,6 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hap.py:0.3.14--py27h5c5a3ab_0" } input: tuple val(meta), path(vcf), path(bed) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index e5673f25f8e..05061747686 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -4,7 +4,6 @@ process HICAP { conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) 'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hicap:1.0.3--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index 471a83f9faa..a09a247298d 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -4,7 +4,6 @@ process HIFIASM { conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hifiasm:0.15.4--h2e03b76_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 1eb027eaae9..9b06b7a26e9 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -5,7 +5,6 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index c78cce35626..eb6ce243c2e 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -6,7 +6,6 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } input: path fasta diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 00ffda4263b..86ac2e3ecc7 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -5,7 +5,6 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hisat2:2.2.1--h1b792b2_3" } input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 39d5525b02e..45b05404d4d 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -4,7 +4,6 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 192afd5292a..0713e96f954 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -5,7 +5,6 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 0e0a85ab597..2f3d135834a 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -4,7 +4,6 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 70a8b66c553..d841629831b 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -5,7 +5,6 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmcopy:0.1.1--h2e03b76_7" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index f5463b6a9dc..91241702964 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -4,7 +4,6 @@ process HMMER_ESLALIMASK { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 00e0b0b99aa..2ed4eb173df 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -4,7 +4,6 @@ process HMMER_ESLREFORMAT { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 43942556f7b..95f08b8677c 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -4,7 +4,6 @@ process HMMER_HMMALIGN { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 0f7477d0089..4277149a6cb 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -4,7 +4,6 @@ process HMMER_HMMBUILD { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 1cfd229f972..bd45fc2d641 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -4,7 +4,6 @@ process HMMER_HMMSEARCH { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmmer:3.3.2--h1b792b2_1" } input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index fdecf3d69d0..9b73da1ce72 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -4,7 +4,6 @@ process HMTNOTE { conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) 'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hmtnote:0.7.2--pyhdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 91f352665ff..3a2b2e78ba0 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -5,7 +5,6 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 280906e0150..5ef5d7397d0 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -5,7 +5,6 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 3868bb47253..ab39d0ae1c4 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -6,7 +6,6 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 71c48d94b89..58a377b0cac 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -5,7 +5,6 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index 8f63cf6b1ff..c4ff5cb05ad 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -5,7 +5,6 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/homer:4.11--pl526hc9558a2_3" } input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 241611a982d..9ce32e8827f 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -5,7 +5,6 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) 'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/hpsuissero:1.0.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index 1f7c019e57d..2950aa108ae 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -4,7 +4,6 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } input: path wigs diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index cd15af79c07..f609a95ecb0 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -5,7 +5,6 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/r-ichorcna:0.3.2--r41hdfd78af_0" } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index 9cbbb3554e0..6ac8771c8fb 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -4,7 +4,6 @@ process IDR { conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/idr:2.0.4.2--py39hcbe4a3b_5" } input: path peaks diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index b9ab7b8da84..d459557ba11 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -4,7 +4,6 @@ process INSTRAIN_PROFILE { conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) 'https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/instrain:1.6.1--pyhdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index 8f48a305af8..fa639a1f1bd 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -4,7 +4,6 @@ process IQTREE { conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) 'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/iqtree:2.1.4_beta--hdcc8f71_0" } input: path alignment diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index eff7679a574..c66d95aa701 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -4,7 +4,6 @@ process ISMAPPER { conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ismapper:2.0.2--pyhdfd78af_1" } input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index 522b51cb3ea..04279bf63ac 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -4,7 +4,6 @@ process ISOSEQ3_CLUSTER { conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index cd7b85d3b07..f13fbced272 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -4,7 +4,6 @@ process ISOSEQ3_REFINE { conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/isoseq3:3.4.0--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 5c23137c903..057f21c23c2 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -4,7 +4,6 @@ process IVAR_CONSENSUS { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index 4e5366e4c38..08e7a0e2dde 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -4,7 +4,6 @@ process IVAR_TRIM { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 7e249b400ee..42415d95fbd 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -4,7 +4,6 @@ process IVAR_VARIANTS { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ivar:1.3.1--h089eab3_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index df247576cd1..9b2bb9fa22d 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -9,7 +9,6 @@ process JUPYTERNOTEBOOK { //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index dac742bf5db..afba70a3c06 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -4,7 +4,6 @@ process KAIJU_KAIJU { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 5de61332ca8..6db1dab219a 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -4,7 +4,6 @@ process KAIJU_KAIJU2KRONA { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h5b5514e_1" } input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 008ecbb79a4..451dd80d68a 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -4,7 +4,6 @@ process KAIJU_KAIJU2TABLE { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/kaiju:1.8.2--h2e03b76_0" } input: tuple val(meta), path(results) diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 5f6fdf18946..e22149fe7fb 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -4,7 +4,6 @@ process KALLISTO_INDEX { conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/kallisto:0.46.2--h4f7b962_1" } input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index cee55eb479c..b3f848160a8 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -4,7 +4,6 @@ process KALLISTOBUSTOOLS_COUNT { conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index e9f6057f807..91abd06f2a6 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -4,7 +4,6 @@ process KALLISTOBUSTOOLS_REF { conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/kb-python:0.27.2--pyhdfd78af_0" } input: path fasta diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 1475c8ced82..42e5b872d68 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -4,7 +4,6 @@ process KAT_HIST { conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) 'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/kat:2.4.2--py38hfc5f9d8_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index 4ce1ff6ff12..93ba30a19b9 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -4,7 +4,6 @@ process KHMER_NORMALIZEBYMEDIAN { conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } input: path pe_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 667d8394bf0..39f28e12468 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -4,7 +4,6 @@ process KHMER_UNIQUEKMERS { conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/khmer:3.0.0a3--py37haa7609a_2" } input: path fasta diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index ae763841d89..244512d97df 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -4,7 +4,6 @@ process KLEBORATE { conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/kleborate:2.1.0--pyhdfd78af_1" } input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 8f7627d361f..c4b30d43812 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -4,7 +4,6 @@ process KRAKEN2_KRAKEN2 { conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index 63bd131c1d8..7617f02bb1b 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -3,7 +3,6 @@ process KRAKENTOOLS_COMBINEKREPORTS { conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 2fc8fca38c3..588f253f8d7 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -5,7 +5,6 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/krakentools:1.2--pyh5e36f6f_0" } input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index dc98f4068f7..e03aa6d57e3 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -5,7 +5,6 @@ process KRONA_KRONADB { conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 8f29594d9cb..a1a3ac1c96f 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -5,7 +5,6 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.8--pl5262hdfd78af_2" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 54a66b791ec..1acde0bcd6c 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -4,7 +4,6 @@ process KRONA_KTIMPORTTEXT { conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.8.1--pl5321hdfd78af_1" } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index f5426208672..bbc19cbe2fe 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -5,7 +5,6 @@ process KRONA_KTUPDATETAXONOMY { conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/krona:2.7.1--pl526_5" } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index c099213edab..dccad1ae27b 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -4,7 +4,6 @@ process LAST_DOTPLOT { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 1dc084500aa..6cc87e06ae2 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -4,7 +4,6 @@ process LAST_LASTAL { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 6b6f13aa2c9..05f4498930a 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -4,7 +4,6 @@ process LAST_LASTDB { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index b54eb31b36f..fc5a22203e9 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -4,7 +4,6 @@ process LAST_MAFCONVERT { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index e1c4e480777..771ac16e716 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -4,7 +4,6 @@ process LAST_MAFSWAP { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index c59b54cec71..9ba02d57294 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -4,7 +4,6 @@ process LAST_POSTMASK { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index eedda24bca7..14ddaa899c0 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -4,7 +4,6 @@ process LAST_SPLIT { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 844b6865881..e08dae12deb 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -4,7 +4,6 @@ process LAST_TRAIN { conda (params.enable_conda ? 'bioconda::last=1250' : null) 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/last:1250--h2e03b76_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index b1c11fc0bb9..ae54135ed3f 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -5,7 +5,6 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/leehom:1.2.15--h29e30f7_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index 29a8bcc476f..8d99ae20d9b 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -4,7 +4,6 @@ process LEGSTA { conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) 'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/legsta:0.5.1--hdfd78af_2" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index dc2182333eb..520f9ba655c 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -4,7 +4,6 @@ process LIMA { conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) 'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/lima:2.2.0--h9ee0642_0" } input: tuple val(meta), path(ccs) diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index ba574037b7d..7dc87bdc48b 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -4,7 +4,6 @@ process LISSERO { conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/lissero:0.4.9--py_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index d6705d21d1b..d14722219a6 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -4,7 +4,6 @@ process LOFREQ_CALL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 16b1cc46994..deff438ce96 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -4,7 +4,6 @@ process LOFREQ_CALLPARALLEL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index b4803d8d4ea..4ef17253c19 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -4,7 +4,6 @@ process LOFREQ_FILTER { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 05ad799a12c..55cd7597854 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -4,7 +4,6 @@ process LOFREQ_INDELQUAL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/lofreq:2.1.5--py38h588ecb2_4" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index d1285d09af8..2365e406054 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -4,7 +4,6 @@ process MACREL_CONTIGS { conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) 'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/macrel:1.1.0--py36hc5360cc_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 939210dff67..f37d75abf86 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -4,7 +4,6 @@ process MACS2_CALLPEAK { conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/macs2:2.2.7.1--py38h4a8c8d9_3" } input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 17acd241ebb..53c65c56d75 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -4,7 +4,6 @@ process MAFFT { conda (params.enable_conda ? "bioconda::mafft=7.490" : null) 'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mafft:7.490--h779adbc_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 2730076e36a..2dbbc35e4d6 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -4,7 +4,6 @@ process MALT_BUILD { conda (params.enable_conda ? "bioconda::malt=0.41" : null) 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/malt:0.41--1" } input: path fastas diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index e67997a212d..cd00e91a1df 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -4,7 +4,6 @@ process MALT_RUN { conda (params.enable_conda ? "bioconda::malt=0.41" : null) 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/malt:0.41--1" } input: tuple val(meta), path(fastqs) diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index 0945300608b..c7cca372cd9 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -4,7 +4,6 @@ process MALTEXTRACT { conda (params.enable_conda ? "bioconda::hops=0.35" : null) 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/hops:0.35--hdfd78af_1" } input: path rma6 diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 43cb7ef7edd..6bb07c5767d 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -4,7 +4,6 @@ process MANTA_CONVERTINVERSION { conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index dc418a55940..348fd201e82 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -4,7 +4,6 @@ process MANTA_GERMLINE { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index ca9bad682d0..e67b3a1082e 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -4,7 +4,6 @@ process MANTA_SOMATIC { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 9cc7c6c828c..cc90cbbc14f 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -4,7 +4,6 @@ process MANTA_TUMORONLY { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/manta:1.6.0--h9ee0642_1" } input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index 319ae407a0e..e650118d99a 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -4,7 +4,6 @@ process MAPDAMAGE2 { conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mapdamage2:2.2.1--pyr40_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index 9c721a6ef71..f999fe8cfe8 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -4,7 +4,6 @@ process MASH_DIST { conda (params.enable_conda ? "bioconda::mash=2.3" : null) 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 940d41b0af4..95dd1d8d1b9 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -4,7 +4,6 @@ process MASH_SCREEN { conda (params.enable_conda ? "bioconda::mash=2.3" : null) 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 12e07bd0769..3cb05ccea04 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -3,7 +3,6 @@ process MASH_SKETCH { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mash:2.3--he348c14_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index 740a483bbfa..e42bb667873 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -4,7 +4,6 @@ process MASHTREE { conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) 'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mashtree:1.2.0--pl526h516909a_0" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 729988f5f7e..204b989d7ff 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -4,7 +4,6 @@ process MAXBIN2 { conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) 'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/maxbin2:2.2.7--he1b5a44_2" } input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index 884d6df3939..ece94cdae68 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -4,7 +4,6 @@ process MAXQUANT_LFQ { conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null) container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" } else { - container ${params.docker_registry ?: 'quay.io/biocontainers'}/maxquant:2.0.3.0--py310hdfd78af_1 } input: diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index 003bff8ecc0..44e62592a1b 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -5,7 +5,6 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) 'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mcroni:1.0.4--pyh5e36f6f_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index cb8d6a463ce..9fbb9608c01 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -4,7 +4,6 @@ process MEDAKA { conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/medaka:1.4.4--py38h130def0_0" } input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 1591f2b6d3b..cb013fd2da4 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -4,7 +4,6 @@ process MEGAHIT { conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index aeb70eb486a..dc4fdd44ecf 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -4,7 +4,6 @@ process MEGAN_DAA2INFO { conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } input: tuple val(meta), path(daa) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 2749a414527..9c65128344d 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -4,7 +4,6 @@ process MEGAN_RMA2INFO { conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/megan:6.21.7--h9ee0642_0" } input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index f350bf6a0e9..ecc3f8147b9 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -4,7 +4,6 @@ process MENINGOTYPE { conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) 'https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/meningotype:0.8.5--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index 305a70ee1fa..196ce99a7e8 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -4,7 +4,6 @@ process MERQURY { conda (params.enable_conda ? "bioconda::merqury=1.3" : null) 'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/merqury:1.3--hdfd78af_1" } input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index afa42c1e1d6..0261588ac21 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -4,7 +4,6 @@ process MERYL_COUNT { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 846129b94a5..7df027e3a9e 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -4,7 +4,6 @@ process MERYL_HISTOGRAM { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index ee06b1436ab..de44b1201a1 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -4,7 +4,6 @@ process MERYL_UNIONSUM { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/meryl:1.3--h87f3376_1" } input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index f67d1894610..a0721192de4 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -4,7 +4,6 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 0cf8565eff1..4e76656afd9 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -4,7 +4,6 @@ process METABAT2_METABAT2 { conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/metabat2:2.15--h986a166_1" } input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index dda987cc9e8..febf47b0460 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -3,7 +3,6 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 63eb904f408..d428ca85b16 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -4,7 +4,6 @@ process METAPHLAN3_METAPHLAN3 { conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/metaphlan:3.0.12--pyhb7b1952_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 970613512c9..cdea4109e94 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -4,7 +4,6 @@ process METHYLDACKEL_EXTRACT { conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index 76c4c35210e..81587c1b97d 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -4,7 +4,6 @@ process METHYLDACKEL_MBIAS { conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/methyldackel:0.6.0--h22771d5_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index d45f1ef16ba..ce491080e7f 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,6 @@ process MINIA { conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/minia:3.2.6--h9a82719_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 64101a295a4..031e1ab167e 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -4,7 +4,6 @@ process MINIASM { conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/miniasm:0.3_r179--h5bf99c6_2" } input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index b05e96b721e..d00147e88f7 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -4,7 +4,6 @@ process MINIMAP2_ALIGN { conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index d03d9fba6b4..1bd6b3fc8f4 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -3,7 +3,6 @@ process MINIMAP2_INDEX { conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/minimap2:2.21--h5bf99c6_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index bc63c6bb7f1..338b2f5e4d0 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -4,7 +4,6 @@ process MLST { conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mlst:2.19.0--hdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index e94fa7431dd..9f5e52bb40c 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -4,7 +4,6 @@ process MOBSUITE_RECON { conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mob_suite:3.0.3--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 19f544cdf1b..5e046b7537b 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,7 +4,6 @@ process MOSDEPTH { conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mosdepth:0.3.3--hdfd78af_1"} input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index 3876bb01436..f57b3f15a13 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -3,7 +3,6 @@ process MOTUS_DOWNLOADDB { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 3394eb6284d..2dbe4c794d4 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -6,7 +6,6 @@ process MOTUS_MERGE { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index 601a8646288..941803de514 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -4,7 +4,6 @@ process MOTUS_PROFILE { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/motus:3.0.1--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index 9a26e9651c9..4f4c7e09239 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -4,7 +4,6 @@ process MSISENSOR_MSI { conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index f8046acadb5..73b6dc817b6 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -4,7 +4,6 @@ process MSISENSOR_SCAN { conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor:0.5--hb3646a4_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index 1266251b086..3c98083220b 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -4,7 +4,6 @@ process MSISENSOR2_MSI { conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index 1ad4fdaa888..3bef5dfe42d 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -4,7 +4,6 @@ process MSISENSOR2_SCAN { conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor2:0.1--hd03093a_0" } input: path fasta diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index 717d4c2c6d8..1066f18c5e9 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -4,7 +4,6 @@ process MSISENSORPRO_MSI_SOMATIC { conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index b7e6a6d37dd..4f5849e646a 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -4,7 +4,6 @@ process MSISENSORPRO_SCAN { conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/msisensor-pro:1.2.0--hfc31af2_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index 9df6a9c6850..ac937ba1ea8 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -4,7 +4,6 @@ process MTNUCRATIO { conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mtnucratio:0.7--hdfd78af_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 468fb6531e0..2a53f1b3ddd 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,7 +3,6 @@ process MULTIQC { conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/multiqc:1.13--pyhdfd78af_0" } input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 715254874de..0123d24b92f 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -4,7 +4,6 @@ process MULTIVCFANALYZER { conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) 'https://depot.galaxyproject.org/singularity/multivcfanalyzer:0.85.2--hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/multivcfanalyzer:0.85.2--hdfd78af_1" } input: path vcfs diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index b2c221563fa..459b6f035c9 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -5,7 +5,6 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 55ad7e55835..dfb63b228de 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -4,7 +4,6 @@ process MUSCLE { conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/muscle:3.8.1551--h7d875b9_6" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index afa2546468a..59931910cfd 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -4,7 +4,6 @@ process MYKROBE_PREDICT { conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) 'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mykrobe:0.11.0--py39h2add14b_1" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 181bcd0e7a4..563559c0f01 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -4,7 +4,6 @@ process NANOLYSE { conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/nanolyse:1.2.0--py_0" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index c53a103396e..c0232ee6241 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -4,7 +4,6 @@ process NANOPLOT { conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) 'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/nanoplot:1.40.0--pyhdfd78af_0" } input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index fc98ea35335..0af824d4161 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -4,7 +4,6 @@ process NCBIGENOMEDOWNLOAD { conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.1--pyh5e36f6f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ncbi-genome-download:0.3.1--pyh5e36f6f_0" } input: val meta diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index fca35a6eb15..697a257cf20 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -4,7 +4,6 @@ process NEXTCLADE_DATASETGET { conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index b8bf3b367d3..54355f71bcb 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -4,7 +4,6 @@ process NEXTCLADE_RUN { conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/nextclade:2.2.0--h9ee0642_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index b21be11c5a5..57221f55f23 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -4,7 +4,6 @@ process NEXTGENMAP { conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) 'https://depot.galaxyproject.org/singularity/nextgenmap%3A0.5.5--hc9558a2_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/nextgenmap:0.5.5--hc9558a2_4" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index a86828ae15b..e5669049df3 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -4,7 +4,6 @@ process NGMASTER { conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) 'https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ngmaster:0.5.8--pyhdfd78af_1" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index b5d5e42b4a0..04f1e7471aa 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -3,7 +3,6 @@ process NGSCHECKMATE_NCM { conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) 'https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ngscheckmate:1.0.0--py27r41hdfd78af_3" } input: path files diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index 243afe191f6..b4f563dc8bc 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -4,7 +4,6 @@ process NUCMER { conda (params.enable_conda ? "bioconda::mummer=3.23" : null) 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mummer:3.23--pl5262h1b792b2_12" } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 8400c2b003f..4cc4c792d20 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -4,7 +4,6 @@ process OPTITYPE { conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/optitype:1.3.5--0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index 080b731899e..999c7384e25 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -4,7 +4,6 @@ process PAIRIX { conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairix:0.3.7--py36h30a8e3e_3" } input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 498915a7ba3..6f6c03aa3fa 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -4,7 +4,6 @@ process PAIRTOOLS_DEDUP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 0d76cb807c7..adccca08cad 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -4,7 +4,6 @@ process PAIRTOOLS_FLIP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 8f83f7a2e17..cd08c694873 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -4,7 +4,6 @@ process PAIRTOOLS_PARSE { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 466c4eda13f..65863886a8f 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -4,7 +4,6 @@ process PAIRTOOLS_RESTRICT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(pairs) diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index a85b466e601..f728bac40f8 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -4,7 +4,6 @@ process PAIRTOOLS_SELECT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index a8ee6767203..18211843e4c 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -4,7 +4,6 @@ process PAIRTOOLS_SORT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pairtools:0.3.0--py37hb9c2fc3_5" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index fac8f2a4853..680e825716c 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -4,7 +4,6 @@ process PANAROO_RUN { conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) 'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/panaroo:1.2.9--pyhdfd78af_0" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 0f1991825c1..a240667350c 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -4,7 +4,6 @@ process PANGOLIN { conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pangolin:4.1.1--pyhdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index c3d31b2da76..679538b841b 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -5,7 +5,6 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) 'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/paraclu:10--h9a82719_1" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 12583067881..07965662e7f 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -4,7 +4,6 @@ process PASTY { conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) 'https://depot.galaxyproject.org/singularity/pasty:1.0.0--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/pasty:1.0.0--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index 5fcecd41d6a..baac00835c9 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -4,7 +4,6 @@ process PBBAM_PBMERGE { conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pbbam:1.7.0--h058f120_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index b8e911abc77..1dd9336f53b 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -4,7 +4,6 @@ process PBCCS { conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) 'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pbccs:6.2.0--h9ee0642_0" } input: tuple val(meta), path(bam), path(pbi) diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 7326459942d..07ec5982ec2 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -4,7 +4,6 @@ process PBPTYPER { conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/pbptyper:1.0.2--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/pbptyper:1.0.2--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index 429f9b0c451..f9b710ccdbf 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -4,7 +4,6 @@ process PEAR { conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) 'https://depot.galaxyproject.org/singularity/pear:0.9.6--h67092d7_8': - "${params.docker_registry ?: 'quay.io/biocontainers'}/pear:0.9.6--h67092d7_8" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index c521bec183c..f3fd2bf1de5 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -4,7 +4,6 @@ process PEDDY { conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/peddy:0.4.8--pyh5e36f6f_0" } input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 3f3ffc6a6e4..fad21cf319f 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -5,7 +5,6 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/phantompeakqualtools:1.2.2--0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index 8bc27e16360..e4d027057ac 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -4,7 +4,6 @@ process PHYLOFLASH { conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) 'https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/phyloflash:3.4--hdfd78af_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 500c7c1ef73..26bc5d26600 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -4,7 +4,6 @@ process PICARD_ADDORREPLACEREADGROUPS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 2d35acadf52..0fe3850703f 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -4,7 +4,6 @@ process PICARD_CLEANSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 75e766024d2..3778691cc53 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -4,7 +4,6 @@ process PICARD_COLLECTHSMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 2c11b44a889..a0e29021da8 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -4,7 +4,6 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index f79d0cb2393..3ff3947c4e2 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -4,7 +4,6 @@ process PICARD_COLLECTWGSMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index a4136418d15..568b08cfc0c 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -4,7 +4,6 @@ process PICARD_CREATESEQUENCEDICTIONARY { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index 6ed748786ad..e3d033d866f 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -4,7 +4,6 @@ process PICARD_CROSSCHECKFINGERPRINTS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(input1) diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index e8d815b5419..2f91f0a0efc 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -4,7 +4,6 @@ process PICARD_FASTQTOSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index d0dc9bb184e..770ab0d2926 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -4,7 +4,6 @@ process PICARD_FILTERSAMREADS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index 003f2c93e20..1b35b218f1c 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -4,7 +4,6 @@ process PICARD_FIXMATEINFORMATION { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 9d8d6c6522b..d6b2f56ebfb 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -4,7 +4,6 @@ process PICARD_LIFTOVERVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index c2336e87d8c..d552ea642bf 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,7 +4,6 @@ process PICARD_MARKDUPLICATES { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index e168c3e8309..ea27ac011bf 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -4,7 +4,6 @@ process PICARD_MERGESAMFILES { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 040f9aedb8b..24ea9afe16c 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -5,7 +5,6 @@ process PICARD_RENAMESAMPLEINVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 3ee512cb3f8..6b54b3423c5 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -4,7 +4,6 @@ process PICARD_SORTSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 1a91a32a1f6..23a216593f2 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -4,7 +4,6 @@ process PICARD_SORTVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/picard:2.27.4--hdfd78af_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index e3b9a71ae3d..14534010738 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -4,7 +4,6 @@ process PINTS_CALLER { conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) 'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pypints:1.1.6--pyh5e36f6f_1" } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index 7e7658ff32c..37b776f1e6b 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -4,7 +4,6 @@ process PIRATE { conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) 'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pirate:1.0.4--hdfd78af_2" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index 3523364ed26..e4de686e785 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -5,7 +5,6 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) 'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/plasmidfinder:2.1.6--py310hdfd78af_1" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index c9a10553be8..a2372f1dafc 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -4,7 +4,6 @@ process PLASMIDID { conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/plasmidid:1.6.5--hdfd78af_0" } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index 7f06526bdd2..ad14cf76fda 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -4,7 +4,6 @@ process PLINK_EXTRACT { conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index fb02426f3f9..41f1fbdf731 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -4,7 +4,6 @@ process PLINK_VCF { conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index 36eafd56606..03c5dca69c9 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -4,7 +4,6 @@ process PLINK2_EXTRACT { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index 447b041859f..a511638957d 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -4,7 +4,6 @@ process PLINK2_SCORE { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(pgen), path(psam), path(pvar) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index 5d5f4dd90a5..c5ca87e58ec 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -4,7 +4,6 @@ process PLINK2_VCF { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/plink2:2.00a2.3--h712d239_1" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 51154763c5e..eea916dc53d 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -4,7 +4,6 @@ process PMDTOOLS_FILTER { conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) 'https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pmdtools:0.60--hdfd78af_5" } input: tuple val(meta), path(bam), path (bai) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index fc253f493fe..40403e1bc93 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -4,7 +4,6 @@ process PORECHOP { conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/porechop:0.2.4--py39h7cff6ad_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 07ed35c26c0..c7e9ce74ec4 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -5,7 +5,6 @@ process PRESEQ_CCURVE { conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 82b07f5611c..15997779de4 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -5,7 +5,6 @@ process PRESEQ_LCEXTRAP { conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/preseq:3.1.2--h445547b_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index df0b18914c8..82191c4fec8 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -4,7 +4,6 @@ process PRINSEQPLUSPLUS { conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) 'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/prinseq-plus-plus:1.2.3--hc90279e_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index e8c9c2ebc31..4af4f090ddc 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -4,7 +4,6 @@ process PRODIGAL { conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index afe19eb8a0e..942eb8ec80c 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -4,7 +4,6 @@ process PROKKA { conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) 'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/prokka:1.14.6--pl5321hdfd78af_4" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index 0db53c5c5cf..92a6abed213 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -4,7 +4,6 @@ process PYCOQC { conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pycoqc:2.5.2--py_0" } input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index b32454034aa..3367f196ac5 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -4,7 +4,6 @@ process PYDAMAGE_ANALYZE { conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index ebb27c83804..bcc57edd0f1 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -4,7 +4,6 @@ process PYDAMAGE_FILTER { conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/pydamage:0.70--pyhdfd78af_0" } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 2962d843b34..3252097f751 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -4,7 +4,6 @@ process QCAT { conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) 'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/qcat:1.1.0--py_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 9eeebdbd3d1..4747efb2688 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -4,7 +4,6 @@ process QUALIMAP_BAMQC { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 41c7906abaa..837a4e14de7 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -4,7 +4,6 @@ process QUALIMAP_BAMQCCRAM { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" } input: tuple val(meta), path(cram), path(crai) diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 1f17835100f..f0e064a1ad5 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -4,7 +4,6 @@ process QUALIMAP_RNASEQ { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/qualimap:2.2.2d--1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index a359be4d1a8..ffa3d2c0f88 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -3,7 +3,6 @@ process QUAST { conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/quast:5.2.0--py39pl5321h2add14b_1" } input: path consensus diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index 3979592c1f4..58273e6c5f0 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -4,7 +4,6 @@ process RACON { conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/racon:1.4.20--h9a82719_1" } input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index a9e66ce6eb3..9ca902b9848 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -4,7 +4,6 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" } input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 87238e690c7..03bdad2f15e 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -4,7 +4,6 @@ process RASUSA { conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) 'https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rasusa:0.3.0--h779adbc_1" } input: tuple val(meta), path(reads), val(genome_size) diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index e0adb2b6bee..8abf363c0d1 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -4,7 +4,6 @@ process RAVEN { conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) 'https://depot.galaxyproject.org/singularity/raven-assembler:1.6.1--h2e03b76_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/raven-assembler:1.6.1--h2e03b76_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index fcb765e11a9..48f4d67bbda 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -3,7 +3,6 @@ process RAXMLNG { conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) 'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/raxml-ng:1.0.3--h32fcf60_0" } input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index e36a59d80a4..5aa7a7a5576 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -4,7 +4,6 @@ process RGI_MAIN { conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) 'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/rgi:5.2.1--pyha8f3691_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 8d364f03fbf..af6baaad4d0 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -4,7 +4,6 @@ process RHOCALL_ANNOTATE { conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/rhocall:0.5.1--py39hbf8eff0_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index f3636c768d8..e2e543dcb20 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -9,7 +9,6 @@ process RMARKDOWNNOTEBOOK { //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index 0affe840d30..6789d641aa5 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -4,7 +4,6 @@ process ROARY { conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) 'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/roary:3.13.0--pl526h516909a_0" } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 61326772ec0..430144a5aef 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -4,7 +4,6 @@ process RSEM_CALCULATEEXPRESSION { conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 8dc2c697ac2..39a68f28e45 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -4,7 +4,6 @@ process RSEM_PREPAREREFERENCE { conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" } input: path fasta, stageAs: "rsem/*" diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index fa332ac1884..b88594f534e 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -4,7 +4,6 @@ process RSEQC_BAMSTAT { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index de69b3dddfb..786ea64d7c9 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -4,7 +4,6 @@ process RSEQC_INFEREXPERIMENT { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index 809ce9034a4..7dcabeb19e7 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -4,7 +4,6 @@ process RSEQC_INNERDISTANCE { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index 49ab8ec9bec..db1725796f4 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -4,7 +4,6 @@ process RSEQC_JUNCTIONANNOTATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 2e45b5b6d09..ebd549fc8cb 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -4,7 +4,6 @@ process RSEQC_JUNCTIONSATURATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index db04fe63518..ca249e5e7f1 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -4,7 +4,6 @@ process RSEQC_READDISTRIBUTION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 4d8120047be..81dad498c47 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -4,7 +4,6 @@ process RSEQC_READDUPLICATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 6cd67900546..4fb43a464a4 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -4,7 +4,6 @@ process RSEQC_TIN { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/rseqc:3.0.1--py37h516909a_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index b180f1e19c3..57f3d9652d3 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -4,7 +4,6 @@ process RTGTOOLS_PEDFILTER { conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 1e3fb3c1213..d3119d9fc73 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -4,7 +4,6 @@ process RTGTOOLS_VCFEVAL { conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/rtg-tools:3.12.1--hdfd78af_0" } input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index edeadbfcf30..ee94cb210a6 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -4,7 +4,6 @@ process SALMON_INDEX { conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } input: path genome_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 67176417d7e..e145fcd0da0 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -4,7 +4,6 @@ process SALMON_QUANT { conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/salmon:1.5.2--h84f40af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 7a69f321380..e25cc136947 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -4,7 +4,6 @@ process SAMBLASTER { conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index b3f1cdb5182..01434418a3e 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_AMPLICONCLIP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index bd2c2ecce60..21f90de13c9 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_BAM2FQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 9d5be730c11..8ec1c0b8014 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_COLLATE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index d9117279ac6..7cda5b46168 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_COLLATEFASTQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index af5f1442a74..b8d733c6348 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index bb6c666c4e6..6fa7c892a99 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_DEPTH { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 30bcbbd223c..8903cb254ca 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_DICT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 26a0494f683..506d890c8e4 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_FAIDX { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 57354397b2a..433ab3fcfcf 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_FASTA { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 52ed57f36b3..be222d39ca3 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_FASTQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index e1d49396ad1..3cc6045a0cb 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_FIXMATE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 9d1617c192d..b80e6cb05a7 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_FLAGSTAT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 0390da63686..ab9b668b447 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_GETRG { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index b62822f449c..e8f3c8b6921 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_IDXSTATS { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index baf7567447c..8f987d455fb 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_INDEX { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 809e1370e3e..eede1fb6df0 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_MARKDUP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index f5d3a491831..96870460947 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_MERGE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index f1014f7f5e2..1e91e69fbef 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_MPILEUP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 29b530ce99c..bb3642efe33 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_SORT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4e63c4859d9..fe9a8e7acc8 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_STATS { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index b589084107e..c07dcefaf38 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,7 +4,6 @@ process SAMTOOLS_VIEW { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/samtools:1.15.1--h1170115_0" } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index a7c92341384..9fc0840f7ba 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -4,7 +4,6 @@ process SCOARY { conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/scoary:1.6.16--py_2" } input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index c7ce7530440..8f6ac9ae359 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -4,7 +4,6 @@ process SCRAMBLE_CLUSTERANALYSIS { conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } input: tuple val(meta), path(clusters) diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 21fd12e4d96..5744350e614 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -4,7 +4,6 @@ process SCRAMBLE_CLUSTERIDENTIFIER { conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/scramble:1.0.1--h779adbc_1" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index 949fb27e449..deccbcec971 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -5,7 +5,6 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" } input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 579f2baf7ef..653388edc1d 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -4,7 +4,6 @@ process SEQKIT_PAIR { conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index e7313339efe..7c934f9ff42 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -4,7 +4,6 @@ process SEQKIT_REPLACE { conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index 7d5d4ab931a..c7b275a2a5e 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -4,7 +4,6 @@ process SEQKIT_SPLIT2 { conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.1.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index 8df0471eec3..5e683226971 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -4,7 +4,6 @@ process SEQKIT_STATS { conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqkit:2.2.0--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index c244bbb70f7..77658ac9afb 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -4,7 +4,6 @@ process SEQSERO2 { conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqsero2:1.2.1--py_0" } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 96717581722..44008c3668c 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -4,7 +4,6 @@ process SEQTK_MERGEPE { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index d30ef006dfd..e3dbbd1e3a0 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -4,7 +4,6 @@ process SEQTK_RENAME { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index 1e1978d48cf..9a0beb30fbf 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -4,7 +4,6 @@ process SEQTK_SAMPLE { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 71a2d484e49..e66b00ff274 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -4,7 +4,6 @@ process SEQTK_SEQ { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 83b923f74ce..cdaba9a1206 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -4,7 +4,6 @@ process SEQTK_SUBSEQ { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqtk:1.3--h5bf99c6_3" } input: path sequences diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index e4d7a04f368..77443f46386 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -4,7 +4,6 @@ process SEQUENZAUTILS_BAM2SEQZ { conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } input: tuple val(meta), path(normalbam), path(tumourbam) diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 653beff80f9..f9fd1251d1e 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -4,7 +4,6 @@ process SEQUENZAUTILS_GCWIGGLE { conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/sequenza-utils:3.0.0--py38h6ed170a_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 9cb2ee2b066..992a50dd259 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -5,7 +5,6 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) 'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/seqwish:0.7.6--h5b5514e_1" } input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 99dfd2cbe2e..df5d5d8aed3 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -4,7 +4,6 @@ process SEROBA_RUN { conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/seroba:1.0.2--pyhdfd78af_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index e465c125aec..737f95901fb 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -4,7 +4,6 @@ process SEXDETERRMINE { conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) 'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/sexdeterrmine:1.1.2--hdfd78af_1" } input: tuple val(meta), path(depth) diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 310a8c0dfed..50507e92619 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -4,7 +4,6 @@ process SHASTA { conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) 'https://depot.galaxyproject.org/singularity/shasta:0.8.0--h7d875b9_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/shasta:0.8.0--h7d875b9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index 4464fb6608a..fa25933e75c 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -4,7 +4,6 @@ process SHIGATYPER { conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/shigatyper:2.0.1--pyhdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 55002cb4c03..75409487121 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -4,7 +4,6 @@ process SHOVILL { conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/shovill:1.1.0--0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index e78e6dbf309..f1aa8cd1f34 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -4,7 +4,6 @@ process SISTR { conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/sistr_cmd:1.1.1--pyh864c0ab_2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index fdb15b73b46..97ba56597e7 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -5,7 +5,6 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) 'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/slimfastq:2.04--h87f3376_2" } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index 785b74bb76f..bf0486d7a96 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -4,7 +4,6 @@ process SNAPALIGNER_ALIGN { conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index 45fd0ff6b08..8fd91112614 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -4,7 +4,6 @@ process SNAPALIGNER_INDEX { conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/snap-aligner:2.0.1--hd03093a_1" } input: path fasta diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index f7b60202392..c3971e18746 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -4,7 +4,6 @@ process SNIPPY_CORE { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_1" } input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index 9264e74be6d..5b3c02c898d 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -4,7 +4,6 @@ process SNIPPY_RUN { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/snippy:4.6.0--hdfd78af_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index f3f99d8645f..68b41edafd8 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -4,7 +4,6 @@ process SNPDISTS { conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) 'https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/snp-dists:0.8.2--h5bf99c6_0" } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 9b8167afd69..5fb008a23d0 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -4,7 +4,6 @@ process SNPEFF { conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/snpeff:5.1--hdfd78af_2" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index da90d3730d2..6ca51ccb286 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -4,7 +4,6 @@ process SNPSIFT_SPLIT { conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/snpsift:4.3.1t--hdfd78af_3" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index 56c31a1745e..fce03657c3f 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -3,7 +3,6 @@ process SNPSITES { conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) 'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/snp-sites:2.5.1--hed695b0_0" } input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index cf650eba96f..377240094b4 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -5,7 +5,6 @@ process SOMALIER_EXTRACT { conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index 23bbe9aa045..5c915c63c8c 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -5,7 +5,6 @@ process SOMALIER_RELATE { conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/somalier:0.2.15--h37c5b7d_0" } input: tuple val(meta), path(extract) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 654a5bc95de..cefdfe62664 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -4,7 +4,6 @@ process SORTMERNA { conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/sortmerna:4.3.4--h9ee0642_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index b409b8183f3..5f7c23d3669 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -4,7 +4,6 @@ process SOURMASH_SKETCH { conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) 'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/sourmash:4.2.4--hdfd78af_0" } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index be655bc18c8..9f9002c4d94 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -4,7 +4,6 @@ process SPADES { conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) 'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/spades:3.15.4--h95f258a_0" } input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index 222462000f9..cd027ebd43a 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -4,7 +4,6 @@ process SPATYPER { conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/spatyper:0.3.3--pyhdfd78af_3" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index 6cf4c64cce4..c9eabb9a924 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -4,7 +4,6 @@ process SRATOOLS_FASTERQDUMP { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" } input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 8e50d3317d9..0bcb618ff51 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -4,7 +4,6 @@ process SRATOOLS_PREFETCH { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/sra-tools:2.11.0--pl5321ha49a11a_3" } input: tuple val(meta), val(id) diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 439b48d02a0..7e99aa8ede6 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -4,7 +4,6 @@ process SRST2_SRST2 { conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) 'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/srst2:0.2.0--py27_2"} input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 3bfe3a035a7..6f934256b08 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -5,7 +5,6 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) 'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ssuissero:1.0.1--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index 682ee58ac73..8dd91080941 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -4,7 +4,6 @@ process STADENIOLIB_SCRAMBLE { conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) 'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/staden_io_lib:1.14.14--h0d9da7e_3" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index b2ec2a2d39b..3baecab3049 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -4,7 +4,6 @@ process STAPHOPIASCCMEC { conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/staphopia-sccmec:1.0.0--hdfd78af_0" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 1a4a01167a5..72a74b7fbd8 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,7 +4,6 @@ process STAR_ALIGN { conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 217a1b70acb..c271711dda3 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -4,7 +4,6 @@ process STAR_GENOMEGENERATE { conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" } input: path fasta diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 5847233ab33..4e8f29113a2 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -4,7 +4,6 @@ process STRANGER { conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) 'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/stranger:0.8.1--pyh5e36f6f_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 6b82116f581..3c3c798c553 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -4,7 +4,6 @@ process STRELKA_GERMLINE { conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index c59bf194522..055350daba9 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -4,7 +4,6 @@ process STRELKA_SOMATIC { conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/strelka:2.9.10--h9ee0642_1" } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 6321d973905..3641a3a26c3 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -4,7 +4,6 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 707d6a88586..31f7d30f307 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -4,7 +4,6 @@ process STRINGTIE_STRINGTIE { conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/stringtie:2.2.1--hecb563c_2" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 79c67644c19..9b657b2993e 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,7 +4,6 @@ process SUBREAD_FEATURECOUNTS { conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/subread:2.0.1--hed695b0_0" } input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 300e744c683..f6e2c7d68a9 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -3,7 +3,6 @@ process SVDB_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" } input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index ae5ff132541..52461e9ef9b 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -4,7 +4,6 @@ process SVDB_QUERY { conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/svdb:2.6.1--py39h5371cbf_0" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index 0348a561656..8e12272cdd4 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -4,7 +4,6 @@ process SVTK_STANDARDIZE { conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) 'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/svtk:0.0.20190615--py37h73a75cf_2" } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 487ad354336..2b79cc28e24 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -4,7 +4,6 @@ process TABIX_BGZIP { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index a7fb8b38927..4dbb8898d94 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,7 +4,6 @@ process TABIX_BGZIPTABIX { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 8e993ac0104..87b6d7937e4 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,7 +4,6 @@ process TABIX_TABIX { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/tabix:1.11--hdfd78af_0" } input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index bf1af7ffa51..55c42b333f1 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -4,7 +4,6 @@ process TAILFINDR { conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" } input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index a0975ebf219..89f8531c607 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -4,7 +4,6 @@ process TBPROFILER_PROFILE { conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) 'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/tb-profiler:3.0.8--pypyh5e36f6f_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 83c1572a426..c91baa77085 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -4,7 +4,6 @@ process TIDDIT_COV { conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) 'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/tiddit:3.0.0--py39h59fae87_1" } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 13280e987ef..d40f2e83d73 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -4,7 +4,6 @@ process TIDDIT_SV { conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) 'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/tiddit:3.1.0--py39h59fae87_1" } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index b13aaa10595..8c86e2c1b53 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,7 +4,6 @@ process TRIMGALORE { conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/trim-galore:0.6.7--hdfd78af_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 2b8200fa43f..966c18a2cd9 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -4,7 +4,6 @@ process TRIMMOMATIC { conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) 'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2': - "${params.docker_registry ?: 'quay.io/biocontainers'}/trimmomatic:0.39--hdfd78af_2" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index 76f3c5a95de..9e3ffe278e4 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -5,7 +5,6 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) 'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedclip:377--h0b8a92a_2" } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 040e714b863..473bf7e411c 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -5,7 +5,6 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedgraphtobigwig:377--h446ed27_1" } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index 301b853f1c4..d7a8439845c 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -5,7 +5,6 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) 'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--ha8a8165_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bedtobigbed:377--ha8a8165_3" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index da6d3dd73de..7527efa52ab 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -5,7 +5,6 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) 'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index e23b84d3139..8904e20ee1b 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -5,7 +5,6 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) 'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-liftover:377--h0b8a92a_3" } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 67c8bbef6fb..59db9a260ef 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -5,7 +5,6 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ucsc-wigtobigwig:377--h0b8a92a_2" } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index 21c523097e5..d0e8db4bf93 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -4,7 +4,6 @@ process ULTRA_ALIGN { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 7824c685dab..9750810cb18 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -4,7 +4,6 @@ process ULTRA_INDEX { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } input: path fasta diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index 242d0a6462c..c13fe9e1ed8 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -4,7 +4,6 @@ process ULTRA_PIPELINE { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index f12ab9f2c2b..0fcfecd13de 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -4,7 +4,6 @@ process UMITOOLS_DEDUP { conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index eb26f70db0e..9df3c875af4 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -4,7 +4,6 @@ process UMITOOLS_EXTRACT { conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/umi_tools:1.1.2--py38h4a8c8d9_0" } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index 1efa6de7056..e0c049daf6e 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -4,7 +4,6 @@ process UNICYCLER { conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/unicycler:0.4.8--py38h8162308_3" } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 95824c37bca..088a0b62a86 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -4,7 +4,6 @@ process UNZIP { conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/p7zip:15.09--h2d50403_4" } input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 2f9e9a4cbfd..0dbaa9a271e 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -4,7 +4,6 @@ process VARDICTJAVA { conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vardict-java:1.8.3--hdfd78af_0" } input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 53684f5e319..1a6699e8231 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -5,7 +5,6 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/variantbam:1.4.4a--h7d7f7ad_5" } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 66b3c800748..f0d1627de69 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -5,7 +5,6 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2db:2020.02.24--hdfd78af_1" } input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 22150d583fc..4bb420db090 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -6,7 +6,6 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" } input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index f66ba468a35..b1c576cb48f 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -4,7 +4,6 @@ process VCFANNO { conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vcfanno:0.3.3--h9ee0642_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 0800969a609..2fba356867a 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -4,7 +4,6 @@ process VCFLIB_VCFBREAKMULTI { conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vcflib:1.0.3--ha025227_0" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index 2da531a459a..d1094f44d0a 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -5,7 +5,6 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vcflib:1.0.3--hecb563c_1" } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index 83218c14c5a..8b85f72ce88 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -4,7 +4,6 @@ process VCFTOOLS { conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/vcftools:0.1.16--he513fc3_4" } input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 736905fdbcf..4deb7c70e4f 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -4,7 +4,6 @@ process VERIFYBAMID_VERIFYBAMID2 { conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/verifybamid2:2.0.1--h19d48f6_8" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 12ecfece25a..4470995414f 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -4,7 +4,6 @@ process VSEARCH_SINTAX { conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index 6c9ebac26db..bebc2ed57c8 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -4,7 +4,6 @@ process VSEARCH_USEARCHGLOBAL { conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - "${params.docker_registry ?: 'quay.io/biocontainers'}/vsearch:2.21.1--h95f258a_0" } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index ac2be0a514e..22f46050b6e 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -4,7 +4,6 @@ process WGSIM { conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) 'https://depot.galaxyproject.org/singularity/wgsim:1.0--h5bf99c6_4': - "${params.docker_registry ?: 'quay.io/biocontainers'}/wgsim:1.0--h5bf99c6_4" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index 2f6cbd91c85..dd2d75b9e80 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -4,7 +4,6 @@ process WHAMG { conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) 'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1': - "${params.docker_registry ?: 'quay.io/biocontainers'}/wham:1.8.0.1.2017.05.03--h8b12597_1" } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index 1bc11490ed4..a8278d1d71b 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -4,7 +4,6 @@ process YARA_INDEX { conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/yara:1.0.2--2" } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 3f6a066ff05..7bc49412d76 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -4,7 +4,6 @@ process YARA_MAPPER { conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : - "${params.docker_registry ?: 'quay.io/biocontainers'}/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" } input: tuple val(meta), path(reads) From 961978ba54d3302049983f1491c75b0d355ccb8e Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 17:21:51 +0200 Subject: [PATCH 16/21] style: Create container_image and container line --- modules/nf-core/abacas/main.nf | 3 ++- modules/nf-core/abricate/run/main.nf | 3 ++- modules/nf-core/abricate/summary/main.nf | 3 ++- modules/nf-core/adapterremoval/main.nf | 3 ++- modules/nf-core/adapterremovalfixprefix/main.nf | 3 ++- modules/nf-core/agrvate/main.nf | 3 ++- modules/nf-core/allelecounter/main.nf | 3 ++- modules/nf-core/ampir/main.nf | 3 ++- modules/nf-core/amplify/predict/main.nf | 3 ++- modules/nf-core/amps/main.nf | 3 ++- modules/nf-core/amrfinderplus/run/main.nf | 3 ++- modules/nf-core/amrfinderplus/update/main.nf | 3 ++- modules/nf-core/angsd/docounts/main.nf | 3 ++- modules/nf-core/antismash/antismashlite/main.nf | 3 ++- .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 3 ++- modules/nf-core/aria2/main.nf | 3 ++- modules/nf-core/ariba/getref/main.nf | 3 ++- modules/nf-core/ariba/run/main.nf | 3 ++- modules/nf-core/arriba/main.nf | 3 ++- modules/nf-core/artic/guppyplex/main.nf | 3 ++- modules/nf-core/artic/minion/main.nf | 3 ++- modules/nf-core/ascat/main.nf | 3 ++- modules/nf-core/assemblyscan/main.nf | 3 ++- modules/nf-core/ataqv/ataqv/main.nf | 3 ++- modules/nf-core/ataqv/mkarv/main.nf | 3 ++- modules/nf-core/atlas/call/main.nf | 3 ++- modules/nf-core/atlas/pmd/main.nf | 3 ++- modules/nf-core/atlas/recal/main.nf | 3 ++- modules/nf-core/atlas/splitmerge/main.nf | 3 ++- modules/nf-core/bakta/main.nf | 3 ++- modules/nf-core/bamaligncleaner/main.nf | 3 ++- modules/nf-core/bamcmp/main.nf | 3 ++- modules/nf-core/bamtools/convert/main.nf | 3 ++- modules/nf-core/bamtools/split/main.nf | 3 ++- modules/nf-core/bamtools/stats/main.nf | 3 ++- modules/nf-core/bamutil/trimbam/main.nf | 3 ++- modules/nf-core/bandage/image/main.nf | 3 ++- modules/nf-core/bbmap/align/main.nf | 3 ++- modules/nf-core/bbmap/bbduk/main.nf | 3 ++- modules/nf-core/bbmap/bbsplit/main.nf | 3 ++- modules/nf-core/bbmap/clumpify/main.nf | 3 ++- modules/nf-core/bbmap/index/main.nf | 3 ++- modules/nf-core/bbmap/pileup/main.nf | 3 ++- modules/nf-core/bcftools/annotate/main.nf | 3 ++- modules/nf-core/bcftools/concat/main.nf | 3 ++- modules/nf-core/bcftools/consensus/main.nf | 3 ++- modules/nf-core/bcftools/convert/main.nf | 3 ++- modules/nf-core/bcftools/filter/main.nf | 3 ++- modules/nf-core/bcftools/index/main.nf | 3 ++- modules/nf-core/bcftools/isec/main.nf | 3 ++- modules/nf-core/bcftools/merge/main.nf | 3 ++- modules/nf-core/bcftools/mpileup/main.nf | 3 ++- modules/nf-core/bcftools/norm/main.nf | 3 ++- modules/nf-core/bcftools/query/main.nf | 3 ++- modules/nf-core/bcftools/reheader/main.nf | 3 ++- modules/nf-core/bcftools/roh/main.nf | 3 ++- modules/nf-core/bcftools/sort/main.nf | 3 ++- modules/nf-core/bcftools/stats/main.nf | 3 ++- modules/nf-core/bcftools/view/main.nf | 3 ++- modules/nf-core/bedtools/bamtobed/main.nf | 3 ++- modules/nf-core/bedtools/complement/main.nf | 3 ++- modules/nf-core/bedtools/genomecov/main.nf | 3 ++- modules/nf-core/bedtools/getfasta/main.nf | 3 ++- modules/nf-core/bedtools/intersect/main.nf | 3 ++- modules/nf-core/bedtools/makewindows/main.nf | 3 ++- modules/nf-core/bedtools/maskfasta/main.nf | 3 ++- modules/nf-core/bedtools/merge/main.nf | 3 ++- modules/nf-core/bedtools/slop/main.nf | 3 ++- modules/nf-core/bedtools/sort/main.nf | 3 ++- modules/nf-core/bedtools/split/main.nf | 3 ++- modules/nf-core/bedtools/subtract/main.nf | 3 ++- modules/nf-core/biobambam/bammerge/main.nf | 3 ++- modules/nf-core/biscuit/align/main.nf | 3 ++- modules/nf-core/biscuit/biscuitblaster/main.nf | 3 ++- modules/nf-core/biscuit/bsconv/main.nf | 3 ++- modules/nf-core/biscuit/epiread/main.nf | 3 ++- modules/nf-core/biscuit/index/main.nf | 3 ++- modules/nf-core/biscuit/mergecg/main.nf | 3 ++- modules/nf-core/biscuit/pileup/main.nf | 3 ++- modules/nf-core/biscuit/qc/main.nf | 3 ++- modules/nf-core/biscuit/vcf2bed/main.nf | 3 ++- modules/nf-core/bismark/align/main.nf | 3 ++- modules/nf-core/bismark/deduplicate/main.nf | 3 ++- modules/nf-core/bismark/genomepreparation/main.nf | 3 ++- modules/nf-core/bismark/methylationextractor/main.nf | 3 ++- modules/nf-core/bismark/report/main.nf | 3 ++- modules/nf-core/bismark/summary/main.nf | 3 ++- modules/nf-core/blast/blastn/main.nf | 3 ++- modules/nf-core/blast/makeblastdb/main.nf | 3 ++- modules/nf-core/blast/tblastn/main.nf | 3 ++- modules/nf-core/bowtie/align/main.nf | 3 ++- modules/nf-core/bowtie/build/main.nf | 3 ++- modules/nf-core/bowtie2/build/main.nf | 3 ++- modules/nf-core/bracken/bracken/main.nf | 3 ++- modules/nf-core/bracken/combinebrackenoutputs/main.nf | 3 ++- modules/nf-core/busco/main.nf | 3 ++- modules/nf-core/bwa/aln/main.nf | 3 ++- modules/nf-core/bwa/index/main.nf | 3 ++- modules/nf-core/bwa/mem/main.nf | 3 ++- modules/nf-core/bwa/sampe/main.nf | 3 ++- modules/nf-core/bwa/samse/main.nf | 3 ++- modules/nf-core/bwamem2/index/main.nf | 3 ++- modules/nf-core/bwamem2/mem/main.nf | 3 ++- modules/nf-core/bwameth/align/main.nf | 3 ++- modules/nf-core/bwameth/index/main.nf | 3 ++- modules/nf-core/cat/cat/main.nf | 3 ++- modules/nf-core/cat/fastq/main.nf | 3 ++- modules/nf-core/centrifuge/centrifuge/main.nf | 3 ++- modules/nf-core/centrifuge/kreport/main.nf | 3 ++- modules/nf-core/checkm/lineagewf/main.nf | 3 ++- modules/nf-core/checkm/qa/main.nf | 3 ++- modules/nf-core/chromap/chromap/main.nf | 3 ++- modules/nf-core/chromap/index/main.nf | 3 ++- modules/nf-core/clonalframeml/main.nf | 3 ++- modules/nf-core/cmseq/polymut/main.nf | 3 ++- modules/nf-core/cnvkit/antitarget/main.nf | 3 ++- modules/nf-core/cnvkit/batch/main.nf | 3 ++- modules/nf-core/cnvkit/reference/main.nf | 3 ++- modules/nf-core/cnvpytor/callcnvs/main.nf | 3 ++- modules/nf-core/cnvpytor/histogram/main.nf | 3 ++- modules/nf-core/cnvpytor/importreaddepth/main.nf | 3 ++- modules/nf-core/cnvpytor/partition/main.nf | 3 ++- modules/nf-core/cnvpytor/view/main.nf | 3 ++- modules/nf-core/controlfreec/assesssignificance/main.nf | 3 ++- modules/nf-core/controlfreec/freec/main.nf | 3 ++- modules/nf-core/controlfreec/freec2bed/main.nf | 3 ++- modules/nf-core/controlfreec/freec2circos/main.nf | 3 ++- modules/nf-core/controlfreec/makegraph/main.nf | 3 ++- modules/nf-core/cooler/cload/main.nf | 3 ++- modules/nf-core/cooler/digest/main.nf | 3 ++- modules/nf-core/cooler/dump/main.nf | 3 ++- modules/nf-core/cooler/merge/main.nf | 3 ++- modules/nf-core/cooler/zoomify/main.nf | 3 ++- modules/nf-core/crumble/main.nf | 3 ++- modules/nf-core/csvtk/concat/main.nf | 3 ++- modules/nf-core/csvtk/split/main.nf | 3 ++- modules/nf-core/custom/dumpsoftwareversions/main.nf | 3 ++- modules/nf-core/custom/getchromsizes/main.nf | 3 ++- modules/nf-core/custom/sratoolsncbisettings/main.nf | 3 ++- modules/nf-core/cutadapt/main.nf | 3 ++- modules/nf-core/damageprofiler/main.nf | 3 ++- modules/nf-core/dastool/dastool/main.nf | 3 ++- modules/nf-core/dastool/fastatocontig2bin/main.nf | 3 ++- modules/nf-core/dastool/scaffolds2bin/main.nf | 3 ++- modules/nf-core/dedup/main.nf | 3 ++- modules/nf-core/deeparg/downloaddata/main.nf | 3 ++- modules/nf-core/deeparg/predict/main.nf | 3 ++- modules/nf-core/deepbgc/download/main.nf | 3 ++- modules/nf-core/deepbgc/pipeline/main.nf | 3 ++- modules/nf-core/deeptools/bamcoverage/main.nf | 3 ++- modules/nf-core/deeptools/computematrix/main.nf | 3 ++- modules/nf-core/deeptools/plotfingerprint/main.nf | 3 ++- modules/nf-core/deeptools/plotheatmap/main.nf | 3 ++- modules/nf-core/deeptools/plotprofile/main.nf | 3 ++- modules/nf-core/delly/call/main.nf | 3 ++- modules/nf-core/diamond/blastp/main.nf | 3 ++- modules/nf-core/diamond/blastx/main.nf | 3 ++- modules/nf-core/diamond/makedb/main.nf | 3 ++- modules/nf-core/dragmap/align/main.nf | 3 ++- modules/nf-core/dragmap/hashtable/main.nf | 3 ++- modules/nf-core/dragonflye/main.nf | 3 ++- modules/nf-core/dshbio/exportsegments/main.nf | 3 ++- modules/nf-core/dshbio/filterbed/main.nf | 3 ++- modules/nf-core/dshbio/filtergff3/main.nf | 3 ++- modules/nf-core/dshbio/splitbed/main.nf | 3 ++- modules/nf-core/dshbio/splitgff3/main.nf | 3 ++- modules/nf-core/ectyper/main.nf | 3 ++- modules/nf-core/elprep/filter/main.nf | 3 ++- modules/nf-core/elprep/merge/main.nf | 3 ++- modules/nf-core/elprep/split/main.nf | 3 ++- modules/nf-core/emboss/seqret/main.nf | 3 ++- modules/nf-core/emmtyper/main.nf | 3 ++- modules/nf-core/endorspy/main.nf | 3 ++- modules/nf-core/ensemblvep/main.nf | 3 ++- modules/nf-core/entrezdirect/esearch/main.nf | 3 ++- modules/nf-core/entrezdirect/esummary/main.nf | 3 ++- modules/nf-core/entrezdirect/xtract/main.nf | 3 ++- modules/nf-core/epang/main.nf | 3 ++- modules/nf-core/expansionhunter/main.nf | 3 ++- modules/nf-core/faqcs/main.nf | 3 ++- modules/nf-core/fargene/main.nf | 3 ++- modules/nf-core/fastani/main.nf | 3 ++- modules/nf-core/fastawindows/main.nf | 3 ++- modules/nf-core/fastp/main.nf | 3 ++- modules/nf-core/fastqc/main.nf | 3 ++- modules/nf-core/fastqscan/main.nf | 3 ++- modules/nf-core/fasttree/main.nf | 3 ++- modules/nf-core/ffq/main.nf | 3 ++- modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 3 ++- modules/nf-core/fgbio/fastqtobam/main.nf | 3 ++- modules/nf-core/fgbio/groupreadsbyumi/main.nf | 3 ++- modules/nf-core/fgbio/sortbam/main.nf | 3 ++- modules/nf-core/fgbio/zipperbams/main.nf | 3 ++- modules/nf-core/filtlong/main.nf | 3 ++- modules/nf-core/flash/main.nf | 3 ++- modules/nf-core/flye/main.nf | 3 ++- modules/nf-core/freebayes/main.nf | 3 ++- modules/nf-core/gamma/gamma/main.nf | 3 ++- modules/nf-core/gappa/examineassign/main.nf | 3 ++- modules/nf-core/gappa/examinegraft/main.nf | 3 ++- modules/nf-core/gappa/examineheattree/main.nf | 3 ++- modules/nf-core/gatk/indelrealigner/main.nf | 3 ++- modules/nf-core/gatk/realignertargetcreator/main.nf | 3 ++- modules/nf-core/gatk/unifiedgenotyper/main.nf | 3 ++- modules/nf-core/gatk4/applybqsr/main.nf | 3 ++- modules/nf-core/gatk4/applyvqsr/main.nf | 3 ++- modules/nf-core/gatk4/baserecalibrator/main.nf | 3 ++- modules/nf-core/gatk4/bedtointervallist/main.nf | 3 ++- modules/nf-core/gatk4/calculatecontamination/main.nf | 3 ++- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 3 ++- modules/nf-core/gatk4/collectreadcounts/main.nf | 3 ++- modules/nf-core/gatk4/collectsvevidence/main.nf | 3 ++- modules/nf-core/gatk4/combinegvcfs/main.nf | 3 ++- modules/nf-core/gatk4/composestrtablefile/main.nf | 3 ++- modules/nf-core/gatk4/createsequencedictionary/main.nf | 3 ++- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 3 ++- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 3 ++- modules/nf-core/gatk4/fastqtosam/main.nf | 3 ++- modules/nf-core/gatk4/filtervarianttranches/main.nf | 3 ++- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 3 ++- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 3 ++- modules/nf-core/gatk4/genomicsdbimport/main.nf | 3 ++- modules/nf-core/gatk4/genotypegvcfs/main.nf | 3 ++- modules/nf-core/gatk4/getpileupsummaries/main.nf | 3 ++- modules/nf-core/gatk4/haplotypecaller/main.nf | 3 ++- modules/nf-core/gatk4/indexfeaturefile/main.nf | 3 ++- modules/nf-core/gatk4/intervallisttobed/main.nf | 3 ++- modules/nf-core/gatk4/intervallisttools/main.nf | 3 ++- modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 3 ++- modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 3 ++- modules/nf-core/gatk4/markduplicates/main.nf | 3 ++- modules/nf-core/gatk4/mergebamalignment/main.nf | 3 ++- modules/nf-core/gatk4/mergemutectstats/main.nf | 3 ++- modules/nf-core/gatk4/mergevcfs/main.nf | 3 ++- modules/nf-core/gatk4/mutect2/main.nf | 3 ++- modules/nf-core/gatk4/printsvevidence/main.nf | 3 ++- modules/nf-core/gatk4/reblockgvcf/main.nf | 3 ++- modules/nf-core/gatk4/revertsam/main.nf | 3 ++- modules/nf-core/gatk4/samtofastq/main.nf | 3 ++- modules/nf-core/gatk4/selectvariants/main.nf | 3 ++- modules/nf-core/gatk4/splitintervals/main.nf | 3 ++- modules/nf-core/gatk4/splitncigarreads/main.nf | 3 ++- modules/nf-core/gatk4/variantfiltration/main.nf | 3 ++- modules/nf-core/gatk4/variantrecalibrator/main.nf | 3 ++- modules/nf-core/gecco/run/main.nf | 3 ++- modules/nf-core/genmap/index/main.nf | 3 ++- modules/nf-core/genmap/mappability/main.nf | 3 ++- modules/nf-core/genmod/annotate/main.nf | 3 ++- modules/nf-core/genmod/compound/main.nf | 3 ++- modules/nf-core/genmod/models/main.nf | 3 ++- modules/nf-core/genmod/score/main.nf | 3 ++- modules/nf-core/genomescope2/main.nf | 3 ++- modules/nf-core/genotyphi/parse/main.nf | 3 ++- modules/nf-core/genrich/main.nf | 3 ++- modules/nf-core/gfaffix/main.nf | 3 ++- modules/nf-core/gffread/main.nf | 3 ++- modules/nf-core/glimpse/chunk/main.nf | 3 ++- modules/nf-core/glnexus/main.nf | 3 ++- modules/nf-core/goat/taxonsearch/main.nf | 3 ++- modules/nf-core/graphmap2/align/main.nf | 3 ++- modules/nf-core/graphmap2/index/main.nf | 3 ++- modules/nf-core/gstama/collapse/main.nf | 3 ++- modules/nf-core/gstama/merge/main.nf | 3 ++- modules/nf-core/gstama/polyacleanup/main.nf | 3 ++- modules/nf-core/gtdbtk/classifywf/main.nf | 3 ++- modules/nf-core/gubbins/main.nf | 3 ++- modules/nf-core/gunc/downloaddb/main.nf | 3 ++- modules/nf-core/gunc/run/main.nf | 3 ++- modules/nf-core/gunzip/main.nf | 3 ++- modules/nf-core/gvcftools/extractvariants/main.nf | 3 ++- modules/nf-core/hamronization/abricate/main.nf | 3 ++- modules/nf-core/hamronization/amrfinderplus/main.nf | 3 ++- 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modules/nf-core/ultra/index/main.nf | 3 ++- modules/nf-core/ultra/pipeline/main.nf | 3 ++- modules/nf-core/umitools/dedup/main.nf | 3 ++- modules/nf-core/umitools/extract/main.nf | 3 ++- modules/nf-core/unicycler/main.nf | 3 ++- modules/nf-core/untar/main.nf | 3 ++- modules/nf-core/unzip/main.nf | 3 ++- modules/nf-core/vardictjava/main.nf | 3 ++- modules/nf-core/variantbam/main.nf | 3 ++- modules/nf-core/vcf2db/main.nf | 3 ++- modules/nf-core/vcf2maf/main.nf | 3 ++- modules/nf-core/vcfanno/main.nf | 3 ++- modules/nf-core/vcflib/vcfbreakmulti/main.nf | 3 ++- modules/nf-core/vcflib/vcfuniq/main.nf | 3 ++- modules/nf-core/vcftools/main.nf | 3 ++- modules/nf-core/verifybamid/verifybamid2/main.nf | 3 ++- modules/nf-core/vsearch/sintax/main.nf | 3 ++- modules/nf-core/vsearch/usearchglobal/main.nf | 3 ++- modules/nf-core/wgsim/main.nf | 3 ++- modules/nf-core/whamg/main.nf | 3 ++- modules/nf-core/yara/index/main.nf | 3 ++- modules/nf-core/yara/mapper/main.nf | 3 ++- 609 files changed, 1218 insertions(+), 609 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index 4a7deb1da6d..fadddcb598f 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -3,7 +3,8 @@ process ABACAS { label 'process_medium' conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) - 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : + def container_image = "/abacas:1.3.1--pl526_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index 85cde9755e8..ff7ef29758d 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -3,7 +3,8 @@ process ABRICATE_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': + def container_image = "/abricate%3A1.0.1--ha8f3691_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index 77ecfc9a912..4397ed7da67 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -3,7 +3,8 @@ process ABRICATE_SUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': + def container_image = "/abricate%3A1.0.1--ha8f3691_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 772b710800e..18c86ffcb24 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -3,7 +3,8 @@ process ADAPTERREMOVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) - 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : + def container_image = "/adapterremoval:2.3.2--hb7ba0dd_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 533655571a3..ab36fcd5622 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -4,7 +4,8 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) - 'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2': + def container_image = "/adapterremovalfixprefix:0.0.5--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 221121a68d9..3906366cdb6 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -3,7 +3,8 @@ process AGRVATE { label 'process_low' conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' : + def container_image = "/agrvate:1.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index b73b32d57be..898f6c33c4d 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -3,7 +3,8 @@ process ALLELECOUNTER { label 'process_low' conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) - 'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' : + def container_image = "/cancerit-allelecount:4.3.0--h41abebc_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index 6c2b1827ef6..0f4011afd05 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -3,7 +3,8 @@ process AMPIR { label 'process_single' conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) - 'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0': + def container_image = "/r-ampir:1.1.0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 2b46c278d3e..62681feec70 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -4,7 +4,8 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) - 'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0': + def container_image = "/amplify:1.0.3--py36hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index d4c39be16be..871b1659fa9 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -2,7 +2,8 @@ process AMPS { label 'process_low' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : + def container_image = "/hops:0.35--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index a4777d9822c..4076eac9b42 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -3,7 +3,8 @@ process AMRFINDERPLUS_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': + def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 25997648646..e49dd098f09 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -3,7 +3,8 @@ process AMRFINDERPLUS_UPDATE { label 'process_single' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0': + def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index adb0eab4d1d..be1094d9ad0 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -3,7 +3,8 @@ process ANGSD_DOCOUNTS { label 'process_low' conda (params.enable_conda ? "bioconda::angsd=0.939" : null) - 'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0': + def container_image = "/angsd:0.939--h468462d_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 02c66e21f9f..a6fe2414007 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -3,7 +3,8 @@ process ANTISMASH_ANTISMASHLITE { label 'process_medium' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : + def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } containerOptions { "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 59e636abb1c..87fdfde1c8d 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,7 +2,8 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { label 'process_single' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' : + def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 8ea20398021..6f388d491c5 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -4,7 +4,8 @@ process ARIA2 { label 'process_single' conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) - 'https://depot.galaxyproject.org/singularity/aria2:1.36.0' : + def container_image = "/aria2:1.36.0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index e8aeb799403..754cb90239b 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -3,7 +3,8 @@ process ARIBA_GETREF { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': + def container_image = "/ariba:2.14.6--py39h67e14b5_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index aee87de1351..4b34b534067 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -3,7 +3,8 @@ process ARIBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - 'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3': + def container_image = "/ariba:2.14.6--py39h67e14b5_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 01f87748e2a..394f60898f5 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -3,7 +3,8 @@ process ARRIBA { label 'process_medium' conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) - 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : + def container_image = "/arriba:2.3.0--haa8aa89_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 4834bc8385f..79c4a678f46 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -3,7 +3,8 @@ process ARTIC_GUPPYPLEX { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : + def container_image = "/artic:1.2.2--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index e7ae81aeb9b..dc121130bc8 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -3,7 +3,8 @@ process ARTIC_MINION { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : + def container_image = "/artic:1.2.2--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index e0e1c260e70..dc514cd0974 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -3,7 +3,8 @@ process ASCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': + def container_image = "/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index af269b84daf..2078c9504e6 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -3,7 +3,8 @@ process ASSEMBLYSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) - 'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' : + def container_image = "/assembly-scan:0.4.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index 5141e66540c..cfb609a3248 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -3,7 +3,8 @@ process ATAQV_ATAQV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' : + def container_image = "/ataqv:1.3.0--py39hccc85d7_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(peak_file) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index cf5d99fd833..c99214d747c 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -2,7 +2,8 @@ process ATAQV_MKARV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - 'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2': + def container_image = "/ataqv:1.3.0--py39hccc85d7_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 66b1b80e0b2..56e6b4dbfc8 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -3,7 +3,8 @@ process ATLAS_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': + def container_image = "/atlas:0.9.9--h082e891_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index 6621acf0ec1..7ba87526473 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -3,7 +3,8 @@ process ATLAS_PMD { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': + def container_image = "/atlas:0.9.9--h082e891_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index 879354024d8..52666da07f1 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -3,7 +3,8 @@ process ATLAS_RECAL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': + def container_image = "/atlas:0.9.9--h082e891_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index 41ee8a2dff7..06f01705c2a 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -3,7 +3,8 @@ process ATLAS_SPLITMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - 'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0': + def container_image = "/atlas:0.9.9--h082e891_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index 51836d6031b..8daf7f458ae 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -3,7 +3,8 @@ process BAKTA { label 'process_medium' conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) - 'https://depot.galaxyproject.org/singularity/bakta:1.5.0--pyhdfd78af_0' : + def container_image = "/bakta:1.5.0--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index b3bf855d85e..85cc97402c5 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -3,7 +3,8 @@ process BAMALIGNCLEANER { label 'process_low' conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) - 'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' : + def container_image = "/bamaligncleaner:0.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 32b9638375c..bcdff49de8b 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -3,7 +3,8 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) - 'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' : + def container_image = "/bamcmp:2.2--h05f6578_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index 49c0f00b972..6a5e5f588a9 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -3,7 +3,8 @@ process BAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : + def container_image = "/bamtools:2.5.1--h9a82719_9" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index b1b1845f608..33496c6ecf2 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -3,7 +3,8 @@ process BAMTOOLS_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) - 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' : + def container_image = "/bamtools:2.5.2--hd03093a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index 75e5940cc46..e52fe198d27 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -3,7 +3,8 @@ process BAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - 'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : + def container_image = "/bamtools:2.5.1--h9a82719_9" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 01013e3364b..16bf907c4a0 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -3,7 +3,8 @@ process BAMUTIL_TRIMBAM { label 'process_single' conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) - 'https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1' : + def container_image = "/bamutil:1.0.15--h2e03b76_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 9fb57b6bb11..6a0e748a79d 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -3,7 +3,8 @@ process BANDAGE_IMAGE { label 'process_low' conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) - 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' : + def container_image = "/bandage:0.8.1--hc9558a2_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index f4cb69a1fd8..652b0694584 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -3,7 +3,8 @@ process BBMAP_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : + def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index bdf4c2443ba..778d5f4e09d 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -3,7 +3,8 @@ process BBMAP_BBDUK { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) - 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : + def container_image = "/bbmap:38.90--he522d1c_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 1bc2d081ac7..4326149c796 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,7 +2,8 @@ process BBMAP_BBSPLIT { label 'process_high' conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) - 'https://depot.galaxyproject.org/singularity/bbmap:38.93--he522d1c_0' : + def container_image = "/bbmap:38.93--he522d1c_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index c2a9829a166..6e4938af95f 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -4,7 +4,8 @@ process BBMAP_CLUMPIFY { label 'process_high_memory' conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) - 'https://depot.galaxyproject.org/singularity/bbmap:38.98--h5c4e2a8_1' : + def container_image = "/bbmap:38.98--h5c4e2a8_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index 7cae94a11d9..c965e523d48 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -3,7 +3,8 @@ process BBMAP_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) - 'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' : + def container_image = "/bbmap:38.92--he522d1c_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 07093a634fe..a4f0e718a32 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -3,7 +3,8 @@ process BBMAP_PILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' : + def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 4f714d4db3a..f9c7d57be26 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_ANNOTATE { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index b2c732ea32e..c1da104cdb2 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_CONCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index 9460ab6b283..f14348608e8 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index f75273e8f92..253ff4a8810 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_CONVERT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 37190046388..794fb4e707c 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index e675e2966f6..6beb2488b19 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 70064f578a5..1b73fe3c565 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_ISEC { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 8fdaf50afcf..8e82b28b4be 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index e464b92675b..8439ab6fd9d 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_MPILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 56945f7c729..bc0d8d2db21 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_NORM { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 6881140e7fc..2035b788d46 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index b5749321521..30b3579890e 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_REHEADER { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 2b391adf4dc..261717f8205 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_ROH { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 9fe0c3507af..ddabb0e3c9e 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 10944af6b80..b5dc76c53a7 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 5f7af0bab37..592345fa1cf 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -3,7 +3,8 @@ process BCFTOOLS_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + def container_image = "/bcftools:1.15.1--h0ea216a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index ed7c6ad1e3a..8316e848755 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_BAMTOBED { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index f3c5546a3ca..6acbba401d5 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_COMPLEMENT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 049a400f0b5..2d3ebabe975 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index d6ab655e192..b0a8b5518b0 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_GETFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path bed diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index 377adae1dd9..e38e0536a63 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_INTERSECT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index e010e6b40c7..c4ec1bf2921 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_MAKEWINDOWS { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' : + def container_image = "/bedtools:2.30.0--h7d7f7ad_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(regions) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index d1ccaceb743..be7a1eaf9ce 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_MASKFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 56004810e70..77783be2894 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index ccc52a12e4b..6ba688688c9 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_SLOP { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 485afd600fd..ac927f57e9b 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_SORT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index a5da2f9fe9e..458f60782d7 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_SPLIT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h468198e_3': + def container_image = "/bedtools:2.30.0--h468198e_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index e2386a1c2b6..3f52e863a54 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -3,7 +3,8 @@ process BEDTOOLS_SUBTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + def container_image = "/bedtools:2.30.0--hc088bd4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index 5f6c56fc806..fb47d41939c 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -3,7 +3,8 @@ process BIOBAMBAM_BAMMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1': + def container_image = "/biobambam:2.0.183--h9f5acd7_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index bb161586aea..f6bfb3a6515 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -3,7 +3,8 @@ process BISCUIT_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 19626f248f6..2687ae908f0 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -3,7 +3,8 @@ process BISCUIT_BLASTER { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index f8bc0bb4660..bfef7866437 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -3,7 +3,8 @@ process BISCUIT_BSCONV { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': + def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index 9649d4999db..9e43bb53ea4 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -3,7 +3,8 @@ process BISCUIT_EPIREAD { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(snp_bed) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 0402f19b26e..415466a7f7c 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -3,7 +3,8 @@ process BISCUIT_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': + def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index 1407a6ec802..c9f565063fc 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -3,7 +3,8 @@ process BISCUIT_MERGECG { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 1a21a43f11f..44c4ca84adb 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -3,7 +3,8 @@ process BISCUIT_PILEUP { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index 962ff532b55..b877e52cbc6 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -3,7 +3,8 @@ process BISCUIT_QC { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - 'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0': + def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 49c87e499f4..0d1dda1320a 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -3,7 +3,8 @@ process BISCUIT_VCF2BED { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0': + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index 76a817190ca..0f5cdc73feb 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -3,7 +3,8 @@ process BISMARK_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : + def container_image = "/bismark:0.23.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index 00eecc00a52..0271ce4bc4c 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -3,7 +3,8 @@ process BISMARK_DEDUPLICATE { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : + def container_image = "/bismark:0.23.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 88de080e969..f851f585f70 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -3,7 +3,8 @@ process BISMARK_GENOMEPREPARATION { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : + def container_image = "/bismark:0.23.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index fbc597274a5..92421fba202 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -3,7 +3,8 @@ process BISMARK_METHYLATIONEXTRACTOR { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : + def container_image = "/bismark:0.23.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 6790ea38b69..84c1f456bfd 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -3,7 +3,8 @@ process BISMARK_REPORT { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : + def container_image = "/bismark:0.23.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 4acf142c197..3b64d4f9b2b 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -2,7 +2,8 @@ process BISMARK_SUMMARY { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : + def container_image = "/bismark:0.23.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path(bam) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index a51f3017599..0c085221505 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -3,7 +3,8 @@ process BLAST_BLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : + def container_image = "/blast:2.12.0--pl5262h3289130_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 03f8293ba0d..e2231c701cf 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -3,7 +3,8 @@ process BLAST_MAKEBLASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : + def container_image = "/blast:2.12.0--pl5262h3289130_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 4e19447602f..b9dad008462 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -3,7 +3,8 @@ process BLAST_TBLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' : + def container_image = "/blast:2.12.0--pl5262h3289130_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 46f2ee9039c..af0ccc20463 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -2,8 +2,9 @@ process BOWTIE_ALIGN { tag "$meta.id" label 'process_high' - def image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) + def container_image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" + container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 2000e64fcf7..88e6cbdbf37 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -3,7 +3,8 @@ process BOWTIE_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) - 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : + def container_image = "/bowtie:1.3.0--py38hed8969a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 53ce8e48408..d22257ef740 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -3,7 +3,8 @@ process BOWTIE2_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) - 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : + def container_image = "/bowtie2:2.4.4--py39hbb4e92a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index c696f517e07..167007f91c8 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -5,7 +5,8 @@ process BRACKEN_BRACKEN { // WARN: Version information not provided by tool on CLI. // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': + def container_image = "/bracken:2.7--py39hc16433a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(kraken_report) diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 228f3d47761..637203e98f1 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,7 +2,8 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { label 'process_low' conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - 'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0': + def container_image = "/bracken:2.7--py39hc16433a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 85410fdd549..d6660e65f20 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -3,7 +3,8 @@ process BUSCO { label 'process_medium' conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) - 'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0': + def container_image = "/busco:5.4.3--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 2c4fcddc7ca..e5a40c89a5f 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -3,7 +3,8 @@ process BWA_ALN { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8' : + def container_image = "/bwa:0.7.17--h5bf99c6_8" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 3e927523661..b4e6bfe93d0 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -3,7 +3,8 @@ process BWA_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : + def container_image = "/bwa:0.7.17--hed695b0_7" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 31397c3cea8..d8f8e3e9c05 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -3,7 +3,8 @@ process BWA_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : + def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index b22324ec152..8e6b5bd1cbe 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -3,7 +3,8 @@ process BWA_SAMPE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : + def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 0f4e486ca98..b36d4e617c9 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -3,7 +3,8 @@ process BWA_SAMSE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' : + def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 37d62e96f1d..b3d4c444e85 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -3,7 +3,8 @@ process BWAMEM2_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) - 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : + def container_image = "/bwa-mem2:2.2.1--he513fc3_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 3a9cd9683ca..ba9daf05533 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -3,7 +3,8 @@ process BWAMEM2_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : + def container_image = "/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index c1313007b66..911f9f388e2 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -3,7 +3,8 @@ process BWAMETH_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : + def container_image = "/bwameth:0.2.2--py_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 85b73b821e0..dcc798831b3 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -3,7 +3,8 @@ process BWAMETH_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : + def container_image = "/bwameth:0.2.2--py_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 0bf0994b7b1..c4f642ece43 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -3,7 +3,8 @@ process CAT_CAT { label 'process_low' conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) - 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : + def container_image = "/pigz:2.3.4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 550e3a95e81..fd69ee5c02c 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,7 +3,8 @@ process CAT_FASTQ { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + def container_image = "/ubuntu:20.04" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 3eeb54d3241..61725726939 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -3,7 +3,8 @@ process CENTRIFUGE_CENTRIFUGE { label 'process_high' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : + def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 50525f26d1b..6669e9640f5 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -3,7 +3,8 @@ process CENTRIFUGE_KREPORT { label 'process_single' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': + def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index ea5e13bfd0d..d02bfdb3e3f 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -3,7 +3,8 @@ process CHECKM_LINEAGEWF { label 'process_medium' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : + def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index ee357a639a0..5ce62a5e9ad 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -3,7 +3,8 @@ process CHECKM_QA { label 'process_low' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : + def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index edfa903189b..04f95c5965c 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -3,7 +3,8 @@ process CHROMAP_CHROMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' : + def container_image = "/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index ab3907f8edf..4f3e44f05be 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -3,7 +3,8 @@ process CHROMAP_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) - 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : + def container_image = "/chromap:0.2.1--hd03093a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index edd2a24db61..31586b0981b 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -3,7 +3,8 @@ process CLONALFRAMEML { label 'process_low' conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) - 'https://depot.galaxyproject.org/singularity/clonalframeml:1.12--h7d875b9_1' : + def container_image = "/clonalframeml:1.12--h7d875b9_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index fd90e526ab2..392fd8bcf23 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -4,7 +4,8 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) - 'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' : + def container_image = "/cmseq:1.0.4--pyhb7b1952_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index 400c8d7656d..ad2f9347794 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -3,7 +3,8 @@ process CNVKIT_ANTITARGET { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': + def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 49a1c58dc67..a1f1ce11d8c 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -3,7 +3,8 @@ process CNVKIT_BATCH { label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' : + def container_image = "/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index cf3fe10f9f9..737918d861f 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -3,7 +3,8 @@ process CNVKIT_REFERENCE { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': + def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index d17bc030dd4..705a7d9be54 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -3,7 +3,8 @@ process CNVPYTOR_CALLCNVS { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 053c05a7ee5..93eea866318 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -3,7 +3,8 @@ process CNVPYTOR_HISTOGRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index bdb89da30d6..3a15bdaf584 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -3,7 +3,8 @@ process CNVPYTOR_IMPORTREADDEPTH { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_file), path(index) diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index 9f548c7dd54..a2b05f424c2 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -3,7 +3,8 @@ process CNVPYTOR_PARTITION { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index e6ed0eb4694..1cd1bfbf886 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -3,7 +3,8 @@ process CNVPYTOR_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0': + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor_files) diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 04800233e7c..20b376df9fe 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -3,7 +3,8 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': + def container_image = "/control-freec:11.6--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 33c1e6009d6..6093d6c40d7 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -3,7 +3,8 @@ process CONTROLFREEC_FREEC { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': + def container_image = "/control-freec:11.6--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index 6efbe1ca315..6b67c7ee559 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -3,7 +3,8 @@ process CONTROLFREEC_FREEC2BED { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': + def container_image = "/control-freec:11.6--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index b00a24d3561..93e9dd97e99 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -3,7 +3,8 @@ process CONTROLFREEC_FREEC2CIRCOS { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': + def container_image = "/control-freec:11.6--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index 23498141697..f47817371f6 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -3,7 +3,8 @@ process CONTROLFREEC_MAKEGRAPH { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': + def container_image = "/control-freec:11.6--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 2b3632e6580..5dd75e6e9a0 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -3,7 +3,8 @@ process COOLER_CLOAD { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : + def container_image = "/cooler:0.8.11--pyh3252c3a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pairs), path(index) diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index b4e21a61cd6..bfc5aa1c069 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -3,7 +3,8 @@ process COOLER_DIGEST { label 'process_medium' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : + def container_image = "/cooler:0.8.11--pyh3252c3a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index ee9563db147..edc075dbc44 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -3,7 +3,8 @@ process COOLER_DUMP { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : + def container_image = "/cooler:0.8.11--pyh3252c3a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index 5be4eb9061b..b266d9940d0 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -3,7 +3,8 @@ process COOLER_MERGE { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : + def container_image = "/cooler:0.8.11--pyh3252c3a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 830e27c2ac7..16ed78a56b3 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -3,7 +3,8 @@ process COOLER_ZOOMIFY { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : + def container_image = "/cooler:0.8.11--pyh3252c3a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index 7d6d78fb6ec..ad85e1ba879 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -3,7 +3,8 @@ process CRUMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) - 'https://depot.galaxyproject.org/singularity/crumble:0.9.0--hb0d9459_1': + def container_image = "/crumble:0.9.0--hb0d9459_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 81d7a0d0336..27f9baa4a9e 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -3,7 +3,8 @@ process CSVTK_CONCAT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : + def container_image = "/csvtk:0.23.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 6f6028514df..7e66f8ab4c1 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -3,7 +3,8 @@ process CSVTK_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : + def container_image = "/csvtk:0.23.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cb4cd830552..c837de10e70 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -3,7 +3,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + def container_image = "/multiqc:1.13--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 121686f400c..d22d04e6079 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -3,7 +3,8 @@ process CUSTOM_GETCHROMSIZES { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 14f35d4f02d..3a2d7041580 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -3,7 +3,8 @@ process CUSTOM_SRATOOLSNCBISETTINGS { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : + def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path('*.mkfg') , emit: ncbi_settings diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 405e98a6650..4f013d2a860 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -3,7 +3,8 @@ process CUTADAPT { label 'process_medium' conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) - 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : + def container_image = "/cutadapt:3.4--py39h38f01e4_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index fe2a0dee638..6573585856c 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -3,7 +3,8 @@ process DAMAGEPROFILER { label 'process_single' conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) - 'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' : + def container_image = "/damageprofiler:1.1--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index fe366727317..9e9d41614ec 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -3,7 +3,8 @@ process DASTOOL_DASTOOL { label 'process_medium' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : + def container_image = "/das_tool:1.1.4--r41hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index e04464e705d..5cfa666f704 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -3,7 +3,8 @@ process DASTOOL_FASTATOCONTIG2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' : + def container_image = "/das_tool:1.1.4--r41hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 5e04e70e265..9972bc56c5a 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -3,7 +3,8 @@ process DASTOOL_SCAFFOLDS2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) - 'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : + def container_image = "/das_tool:1.1.3--r41hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index 3740ffb883c..3f34dba9178 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -3,7 +3,8 @@ process DEDUP { label 'process_single' conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) - 'https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1' : + def container_image = "/dedup:0.12.8--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index b02f7388c7f..f7aaf9e8b63 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,7 +2,8 @@ process DEEPARG_DOWNLOADDATA { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : + def container_image = "/deeparg:1.0.2--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index dfd6f333944..2bb07b8a2e1 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -3,7 +3,8 @@ process DEEPARG_PREDICT { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : + def container_image = "/deeparg:1.0.2--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 0dc2a71ed1f..be5f69f6ac7 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -2,7 +2,8 @@ process DEEPBGC_DOWNLOAD { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': + def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index a1e150059a2..1986cb0820e 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -3,7 +3,8 @@ process DEEPBGC_PIPELINE { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - 'https://depot.galaxyproject.org/singularity/deepbgc:0.1.30--pyhb7b1952_1': + def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index c256d28bff9..f19eab725e8 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -3,7 +3,8 @@ process DEEPTOOLS_BAMCOVERAGE { label 'process_low' conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0': + def container_image = "/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 45d65d2484b..6b733606618 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -3,7 +3,8 @@ process DEEPTOOLS_COMPUTEMATRIX { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : + def container_image = "/deeptools:3.5.1--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index 1982a599388..d5396ba699f 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -3,7 +3,8 @@ process DEEPTOOLS_PLOTFINGERPRINT { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : + def container_image = "/deeptools:3.5.1--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index ed50b7b5e2a..a997abb7b9f 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -3,7 +3,8 @@ process DEEPTOOLS_PLOTHEATMAP { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : + def container_image = "/deeptools:3.5.1--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index d31ab9f71cd..b8fc60c43dd 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -3,7 +3,8 @@ process DEEPTOOLS_PLOTPROFILE { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : + def container_image = "/deeptools:3.5.1--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index 0ddfdfdc09d..b2a1c9d09a3 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -3,7 +3,8 @@ process DELLY_CALL { label 'process_medium' conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) - 'https://depot.galaxyproject.org/singularity/delly:1.1.5--h358d541_0' : + def container_image = "/delly:1.1.5--h358d541_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(exclude_bed) diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index a0a725148b0..68d3cb82f12 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -3,7 +3,8 @@ process DIAMOND_BLASTP { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : + def container_image = "/diamond:2.0.15--hb97b32f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 4e5159bd3ef..6b170d05506 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -3,7 +3,8 @@ process DIAMOND_BLASTX { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : + def container_image = "/diamond:2.0.15--hb97b32f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index 9cfed59c06f..52994d4f82d 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -3,7 +3,8 @@ process DIAMOND_MAKEDB { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : + def container_image = "/diamond:2.0.15--hb97b32f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index a76735ffcb7..ebd2967aa1b 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -3,7 +3,8 @@ process DRAGMAP_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0': + def container_image = "/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index b364e8d43d7..b665dee6817 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -3,7 +3,8 @@ process DRAGMAP_HASHTABLE { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0': + def container_image = "/dragmap:1.2.1--hd4ca14e_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index fbfe1c62db0..de209c7bea4 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -3,7 +3,8 @@ process DRAGONFLYE { label 'process_medium' conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) - 'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' : + def container_image = "/dragonflye:1.0.11--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index ec060abbd58..24ed2cab53f 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -3,7 +3,8 @@ process DSHBIO_EXPORTSEGMENTS { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : + def container_image = "/dsh-bio:2.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 3299b66a9fc..e1723f5a864 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -3,7 +3,8 @@ process DSHBIO_FILTERBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : + def container_image = "/dsh-bio:2.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index c3d46b2725a..054b715e75e 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -3,7 +3,8 @@ process DSHBIO_FILTERGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : + def container_image = "/dsh-bio:2.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index bae090ae854..ace2aadbd42 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -3,7 +3,8 @@ process DSHBIO_SPLITBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : + def container_image = "/dsh-bio:2.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 09959398983..7be6819fc7b 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -3,7 +3,8 @@ process DSHBIO_SPLITGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - 'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' : + def container_image = "/dsh-bio:2.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 0b57919758b..655b9777a6f 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -3,7 +3,8 @@ process ECTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) - 'https://depot.galaxyproject.org/singularity/ectyper:1.0.0--pyhdfd78af_1' : + def container_image = "/ectyper:1.0.0--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 9573b30af0e..c4b76804921 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -3,7 +3,8 @@ process ELPREP_FILTER { label 'process_high' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': + def container_image = "/elprep:5.1.2--he881be0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index 1fcd11a9330..0175dddc605 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -3,7 +3,8 @@ process ELPREP_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': + def container_image = "/elprep:5.1.2--he881be0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 3465a68d741..2cd76a3fd3c 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -3,7 +3,8 @@ process ELPREP_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': + def container_image = "/elprep:5.1.2--he881be0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index c9dabd6b20d..5d456f25de2 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -3,7 +3,8 @@ process EMBOSS_SEQRET { label 'process_single' conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) - 'https://depot.galaxyproject.org/singularity/emboss:6.6.0--hf657eab_5': + def container_image = "/emboss:6.6.0--hf657eab_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 3ea8545a173..e31a6e3a60c 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -3,7 +3,8 @@ process EMMTYPER { label 'process_low' conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) - 'https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0' : + def container_image = "/emmtyper:0.2.0--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index a783b1dc8b3..87cf4968cf9 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -3,7 +3,8 @@ process ENDORSPY { label 'process_low' conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) - 'https://depot.galaxyproject.org/singularity/endorspy:0.4--hdfd78af_0': + def container_image = "/endorspy:0.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index c45873f64d6..e46599352ad 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -3,7 +3,8 @@ process ENSEMBLVEP { label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) - 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' : + def container_image = "/ensembl-vep:106.1--pl5321h4a94de4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 0a3e77d55c1..8506407bc5a 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -3,7 +3,8 @@ process ENTREZDIRECT_ESEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': + def container_image = "/entrez-direct:16.2--he881be0_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(term) diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index 4127e977c30..ee933331997 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -3,7 +3,8 @@ process ENTREZDIRECT_ESUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': + def container_image = "/entrez-direct:16.2--he881be0_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(uid), path(uids_file) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index 0384254d5e7..588926a6412 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -3,7 +3,8 @@ process ENTREZDIRECT_XTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': + def container_image = "/entrez-direct:16.2--he881be0_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(xml_input) diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index c365088c8a9..77495e9e490 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -3,7 +3,8 @@ process EPANG { label 'process_high' conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) - 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': + def container_image = "/epa-ng:0.3.8--h9a82719_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(queryaln) diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index 73620c85e12..c165b2934bf 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -3,7 +3,8 @@ process EXPANSIONHUNTER { label 'process_low' conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) - 'https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0' : + def container_image = "/expansionhunter:4.0.2--he785bd8_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index ee3456e60b8..8d21e30489e 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -3,7 +3,8 @@ process FAQCS { label 'process_medium' conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) - 'https://depot.galaxyproject.org/singularity/faqcs%3A2.10--r41h9a82719_2' : + def container_image = "/faqcs%3A2.10--r41h9a82719_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index 179ea874d9c..f830e6306cc 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -4,7 +4,8 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) - 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : + def container_image = "/fargene:0.1--py27h21c881e_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index c72611d2cae..6a0cb361bc4 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -3,7 +3,8 @@ process FASTANI { label 'process_medium' conda (params.enable_conda ? "bioconda::fastani=1.32" : null) - 'https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0' : + def container_image = "/fastani:1.32--he1c1bb9_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query) diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index b7e1aac576c..853c76c4f16 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -3,7 +3,8 @@ process FASTAWINDOWS { label 'process_low' conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) - 'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0': + def container_image = "/fasta_windows:0.2.4--hec16e2b_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 60b5dac75d9..0305d1b938a 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -3,7 +3,8 @@ process FASTP { label 'process_medium' conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) - 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : + def container_image = "/fastp:0.23.2--h79da9fb_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 8b9f6616f57..bfa74600fc5 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -3,7 +3,8 @@ process FASTQC { label 'process_medium' conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : + def container_image = "/fastqc:0.11.9--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index 53545ca5a06..ac1ccd1a409 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -3,7 +3,8 @@ process FASTQSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) - 'https://depot.galaxyproject.org/singularity/fastq-scan:0.4.4--h7d875b9_0' : + def container_image = "/fastq-scan:0.4.4--h7d875b9_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 66ff760a339..01760e3f274 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -2,7 +2,8 @@ process FASTTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) - 'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' : + def container_image = "/fasttree:2.1.10--h516909a_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 6187e889758..118f087dc84 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -3,7 +3,8 @@ process FFQ { label 'process_low' conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) - 'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0': + def container_image = "/ffq:0.2.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index fbb1a3f1807..92b60f320a9 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -3,7 +3,8 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + def container_image = "/fgbio:2.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index c3a9ed7ac03..eede7f7a899 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -3,7 +3,8 @@ process FGBIO_FASTQTOBAM { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + def container_image = "/fgbio:2.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index ac30aa8bfd3..4b57de9ffed 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -3,7 +3,8 @@ process FGBIO_GROUPREADSBYUMI { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + def container_image = "/fgbio:2.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(taggedbam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index 61fc7c25495..4516f3f9f83 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -3,7 +3,8 @@ process FGBIO_SORTBAM { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + def container_image = "/fgbio:2.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index ba3fb6dfb21..35195aff6cf 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -3,7 +3,8 @@ process FGBIO_ZIPPERBAMS { label 'process_single' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' : + def container_image = "/fgbio:2.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(unmapped_bam) diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index 95cc86f3d66..f0e1e060a7f 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -3,7 +3,8 @@ process FILTLONG { label 'process_low' conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) - 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : + def container_image = "/filtlong:0.2.1--h9a82719_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index 11fcf6f472d..30f26057056 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -2,7 +2,8 @@ process FLASH { tag "$meta.id" label 'process_medium' - 'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' : + def container_image = "/flash:1.2.11--hed695b0_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index c773757f8c1..68ca1e737c3 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -3,7 +3,8 @@ process FLYE { label 'process_high' conda (params.enable_conda ? "bioconda::flye=2.9" : null) - 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' : + def container_image = "/flye:2.9--py39h6935b12_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 406c0c37b4a..86915263945 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -3,7 +3,8 @@ process FREEBAYES { label 'process_low' conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) - 'https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3' : + def container_image = "/freebayes:1.3.5--py38ha193a2f_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 5e1869603ad..b53de55b41b 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -5,7 +5,8 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) - 'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0': + def container_image = "/gamma%3A2.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index ad675a4b057..fb635ca9a68 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -3,7 +3,8 @@ process GAPPA_EXAMINEASSIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': + def container_image = "/gappa:0.8.0--h9a82719_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 6a63e115ae1..7489e67447b 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -3,7 +3,8 @@ process GAPPA_EXAMINEGRAFT { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': + def container_image = "/gappa:0.8.0--h9a82719_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 5c709401dd2..19be805b1d7 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -3,7 +3,8 @@ process GAPPA_EXAMINEHEATTREE { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': + def container_image = "/gappa:0.8.0--h9a82719_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 36dff0d20a9..0b3aedacce1 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -3,7 +3,8 @@ process GATK_INDELREALIGNER { label 'process_single' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': + def container_image = "/gatk:3.5--hdfd78af_11" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index 400746be8e2..eae92b37788 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -3,7 +3,8 @@ process GATK_REALIGNERTARGETCREATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': + def container_image = "/gatk:3.5--hdfd78af_11" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 82ce641c57c..8709e15f8e6 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -3,7 +3,8 @@ process GATK_UNIFIEDGENOTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - 'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11': + def container_image = "/gatk:3.5--hdfd78af_11" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index ae4e189080d..00e3c1b32fe 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -3,7 +3,8 @@ process GATK4_APPLYBQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 21c1b43c855..966bc6b8bc3 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -3,7 +3,8 @@ process GATK4_APPLYVQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index e0cd109ed65..fc1b3ef14b3 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -3,7 +3,8 @@ process GATK4_BASERECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 3c553a6a387..a80400dc53f 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -3,7 +3,8 @@ process GATK4_BEDTOINTERVALLIST { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 737d295033d..d106cdf682d 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -3,7 +3,8 @@ process GATK4_CALCULATECONTAMINATION { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index b09c91f8ca4..3a2a5f81af1 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -3,7 +3,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 6bb2c62f2fa..a77a18804be 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -3,7 +3,8 @@ process GATK4_COLLECTREADCOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 19beae65b6c..bd8556a7cf8 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -3,7 +3,8 @@ process GATK4_COLLECTSVEVIDENCE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 10cb3e27afe..2dc9563b8eb 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -3,7 +3,8 @@ process GATK4_COMBINEGVCFS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index a45f8e0c16a..574aa1c99ab 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -3,7 +3,8 @@ process GATK4_COMPOSESTRTABLEFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 1d7096b2a35..4455f99dd1d 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -3,7 +3,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 704f2df1cf5..32cffc7b2d0 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -3,7 +3,8 @@ process GATK4_CREATESOMATICPANELOFNORMALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 9e0fca3fde4..758feceb294 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -3,7 +3,8 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 58c0b776bb9..38d11641871 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -3,7 +3,8 @@ process GATK4_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 6bc7c1bac14..bbfed0f908b 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -3,7 +3,8 @@ process GATK4_FILTERVARIANTTRANCHES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 6236c110d12..ea8975576d3 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -3,7 +3,8 @@ process GATK4_GATHERBQSRREPORTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index a402f06e078..e6339d44c19 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -3,7 +3,8 @@ process GATK4_GATHERPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index f6651004df1..86c09bcbb0e 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -3,7 +3,8 @@ process GATK4_GENOMICSDBIMPORT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index d0140d51977..0ce81fb2001 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -3,7 +3,8 @@ process GATK4_GENOTYPEGVCFS { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 18535b7b79f..ec5e06d8d85 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -3,7 +3,8 @@ process GATK4_GETPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 956e0399512..9081413b7a9 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -3,7 +3,8 @@ process GATK4_HAPLOTYPECALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 4e7699851d4..1ec648510d6 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -3,7 +3,8 @@ process GATK4_INDEXFEATUREFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 72db1e0cd8a..a37c069faf2 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -3,7 +3,8 @@ process GATK4_INTERVALLISTTOBED { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index b9b70dd6815..79b6715e9f6 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -3,7 +3,8 @@ process GATK4_INTERVALLISTTOOLS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 8d617a97ec4..c5e3e67faa3 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -3,7 +3,8 @@ process GATK4_LEARNREADORIENTATIONMODEL { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 9cbd4906629..c47f9fc7bba 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -3,7 +3,8 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 371856afc8c..578b26d786c 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -3,7 +3,8 @@ process GATK4_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 8db32b45196..c1768fe695f 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -3,7 +3,8 @@ process GATK4_MERGEBAMALIGNMENT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index f06a0fe0fde..075d08bb8b9 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -3,7 +3,8 @@ process GATK4_MERGEMUTECTSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 0a4bf92b038..176e15833c2 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -3,7 +3,8 @@ process GATK4_MERGEVCFS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index dfdf62bd39d..0e850eb4dad 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -3,7 +3,8 @@ process GATK4_MUTECT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 8cdc06996be..0182239e5f8 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -3,7 +3,8 @@ process GATK4_PRINTSVEVIDENCE { label 'process_single' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 395a5e2ec9b..a66b578ed9b 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -3,7 +3,8 @@ process GATK4_REBLOCKGVCF { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 39a95272f4b..00d8100f647 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -3,7 +3,8 @@ process GATK4_REVERTSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index f7ebf57bdf0..353bab8d6e0 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -3,7 +3,8 @@ process GATK4_SAMTOFASTQ { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 7f234828af1..2a2c1cb94ce 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -3,7 +3,8 @@ process GATK4_SELECTVARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index be6091e08a0..1421a6f4171 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -3,7 +3,8 @@ process GATK4_SPLITINTERVALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 230973d87eb..19d1b4902a8 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -3,7 +3,8 @@ process GATK4_SPLITNCIGARREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 01684cf0940..cc3a8d9f79f 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -3,7 +3,8 @@ process GATK4_VARIANTFILTRATION { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index b660abae359..37659a88062 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -3,7 +3,8 @@ process GATK4_VARIANTRECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index c10e98d6321..9ae078fa093 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -3,7 +3,8 @@ process GECCO_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) - 'https://depot.galaxyproject.org/singularity/gecco:0.9.2--pyhdfd78af_0': + def container_image = "/gecco:0.9.2--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(hmm) diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index ab22cb798e7..9bec567251f 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -3,7 +3,8 @@ process GENMAP_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : + def container_image = "/genmap:1.3.0--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index 9ebd1663cc0..c1b5e099307 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -3,7 +3,8 @@ process GENMAP_MAPPABILITY { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' : + def container_image = "/genmap:1.3.0--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index 37b1af4a7eb..e65e44b2343 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -3,7 +3,8 @@ process GENMOD_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 881b4e53b5a..9ec37befba1 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -3,7 +3,8 @@ process GENMOD_COMPOUND { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 96cb4c5517e..e4b49ae084c 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -3,7 +3,8 @@ process GENMOD_MODELS { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) - 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index e376d2d82ba..d1d843d3717 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -3,7 +3,8 @@ process GENMOD_SCORE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - 'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0': + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index e55747a2e59..2773643c78f 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -3,7 +3,8 @@ process GENOMESCOPE2 { label 'process_low' conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) - 'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5': + def container_image = "/genomescope2:2.0--py310r41hdfd78af_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index c57cde1dd45..8263cb2bbee 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -3,7 +3,8 @@ process GENOTYPHI_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) - 'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1': + def container_image = "/genotyphi:1.9.1--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 274b3474e3f..863b0b1b4f6 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -3,7 +3,8 @@ process GENRICH { label 'process_high' conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) - 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' : + def container_image = "/genrich:0.6.1--h5bf99c6_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(treatment_bam) diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index d1b21640899..ea4b0e69b2f 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -4,7 +4,8 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) - 'https://depot.galaxyproject.org/singularity/gfaffix:0.1.4--hec16e2b_0' : + def container_image = "/gfaffix:0.1.4--hec16e2b_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 2c459b68724..5ec23c1ea59 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -3,7 +3,8 @@ process GFFREAD { label 'process_low' conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) - 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : + def container_image = "/gffread:0.12.1--h8b12597_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index 110efddc399..dcc25bb85c6 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -3,7 +3,8 @@ process GLIMPSE_CHUNK { label 'process_medium' conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2': + def container_image = "/glimpse-bio:1.1.1--h2ce4488_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 2480c1fde69..1f07001b8bb 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -3,7 +3,8 @@ process GLNEXUS { label 'process_medium' conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) - 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : + def container_image = "/glnexus:1.4.1--h40d77a6_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index 777606f4793..f23b379599d 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -3,7 +3,8 @@ process GOAT_TAXONSEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) - 'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0': + def container_image = "/goat:0.2.0--h92d785c_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index c2f9de78e0c..db2ee1831ca 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -4,7 +4,8 @@ process GRAPHMAP2_ALIGN { tag "$meta.id" conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : + def container_image = "/graphmap:0.6.3--he513fc3_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index f6c329c7ec1..7ed53ed9118 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -2,7 +2,8 @@ process GRAPHMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' : + def container_image = "/graphmap:0.6.3--he513fc3_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index 6845650c5cf..61f3016bc74 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -3,7 +3,8 @@ process GSTAMA_COLLAPSE { label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : + def container_image = "/gs-tama:1.0.3--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 26885f82b02..42342b6ceb6 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -3,7 +3,8 @@ process GSTAMA_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' : + def container_image = "/gs-tama:1.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index a34a1561345..666fb5e673d 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -3,7 +3,8 @@ process GSTAMA_POLYACLEANUP { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0': + def container_image = "/gs-tama:1.0.3--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 0ae59ebb639..a0eaba9772b 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -4,7 +4,8 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) - 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' : + def container_image = "/gtdbtk:1.5.0--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path("bins/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 197df72a0b6..380195c635f 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -2,7 +2,8 @@ process GUBBINS { label 'process_medium' conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) - 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : + def container_image = "/gubbins:3.0.0--py39h5bf99c6_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 0d242f56565..ecbe459754d 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -3,7 +3,8 @@ process GUNC_DOWNLOADDB { label 'process_single' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : + def container_image = "/gunc:1.0.5--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index 3906c0fe047..b7890ae56a1 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -3,7 +3,8 @@ process GUNC_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' : + def container_image = "/gunc:1.0.5--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 698ac0f5feb..43707a3288a 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -3,7 +3,8 @@ process GUNZIP { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + def container_image = "/ubuntu:20.04" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index f9545489d96..5b2c5ff123a 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -3,7 +3,8 @@ process GVCFTOOLS_EXTRACTVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) - 'https://depot.galaxyproject.org/singularity/gvcftools:0.17.0--he941832_3': + def container_image = "/gvcftools:0.17.0--he941832_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 2d514e05d61..5593f922bf8 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -3,7 +3,8 @@ process HAMRONIZATION_ABRICATE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index 90317f9140c..127914c43b3 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -3,7 +3,8 @@ process HAMRONIZATION_AMRFINDERPLUS { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 2609f20a01d..ddc729a2ac2 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -3,7 +3,8 @@ process HAMRONIZATION_DEEPARG { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index e0fdb675093..cd687f52843 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -3,7 +3,8 @@ process HAMRONIZATION_FARGENE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index 010a47e15b0..99427bd39ed 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -3,7 +3,8 @@ process HAMRONIZATION_RGI { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index a25837f1a03..dddb66b9491 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -2,7 +2,8 @@ process HAMRONIZATION_SUMMARIZE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path(reports) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index d472319259c..fe711f44e95 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -3,7 +3,8 @@ process HAPLOCHECK { label 'process_low' conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) - 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': + def container_image = "/haplocheck:1.3.3--h4a94de4_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 5b114b08179..0dbbcb06ea3 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -3,7 +3,8 @@ process HAPLOGREP2_CLASSIFY { label 'process_low' conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) - 'https://depot.galaxyproject.org/singularity/haplogrep:2.4.0--hdfd78af_0': + def container_image = "/haplogrep:2.4.0--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index d546611f776..3e400e6d574 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -4,7 +4,8 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': + def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index 06324578e03..a4b82bab5b3 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -4,7 +4,8 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': + def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(bed) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 05061747686..f13df93c87d 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -3,7 +3,8 @@ process HICAP { label 'process_low' conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) - 'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' : + def container_image = "/hicap:1.0.3--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index a09a247298d..7d72bd88f1b 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -3,7 +3,8 @@ process HIFIASM { label 'process_high' conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) - 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' : + def container_image = "/hifiasm:0.15.4--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 9b06b7a26e9..15e8a3dd70f 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -4,7 +4,8 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' : + def container_image = "/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index eb6ce243c2e..d58d2b736d0 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -5,7 +5,8 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : + def container_image = "/hisat2:2.2.1--h1b792b2_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 86ac2e3ecc7..2fb690b7846 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -4,7 +4,8 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : + def container_image = "/hisat2:2.2.1--h1b792b2_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 45b05404d4d..5e8ee115f71 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -3,7 +3,8 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 0713e96f954..63f41c3544a 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -4,7 +4,8 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 2f3d135834a..ed23dcc6f67 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -3,7 +3,8 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7': + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index d841629831b..436249fbfe8 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -4,7 +4,8 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' : + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index 91241702964..f017436ee23 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -3,7 +3,8 @@ process HMMER_ESLALIMASK { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': + def container_image = "/hmmer:3.3.2--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 2ed4eb173df..2d3d3bf9bc1 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -3,7 +3,8 @@ process HMMER_ESLREFORMAT { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': + def container_image = "/hmmer:3.3.2--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 95f08b8677c..8a1fdcf62ec 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -3,7 +3,8 @@ process HMMER_HMMALIGN { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : + def container_image = "/hmmer:3.3.2--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 4277149a6cb..4b9eedd1c5c 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -3,7 +3,8 @@ process HMMER_HMMBUILD { label 'process_low' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2': + def container_image = "/hmmer:3.3.2--h87f3376_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index bd45fc2d641..1f66d3174db 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -3,7 +3,8 @@ process HMMER_HMMSEARCH { label 'process_medium' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : + def container_image = "/hmmer:3.3.2--h1b792b2_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index 9b73da1ce72..0171ce80b52 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -3,7 +3,8 @@ process HMTNOTE { label 'process_low' conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) - 'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0': + def container_image = "/hmtnote:0.7.2--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 3a2b2e78ba0..c2048517257 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -4,7 +4,8 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : + def container_image = "/homer:4.11--pl526hc9558a2_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 5ef5d7397d0..f276fc22ce4 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -4,7 +4,8 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : + def container_image = "/homer:4.11--pl526hc9558a2_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index ab39d0ae1c4..91398f53a32 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,7 +5,8 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' : + def container_image = "/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 58a377b0cac..5d32793c996 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -4,7 +4,8 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : + def container_image = "/homer:4.11--pl526hc9558a2_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index c4ff5cb05ad..a9b6e421165 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -4,7 +4,8 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' : + def container_image = "/homer:4.11--pl526hc9558a2_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 9ce32e8827f..c1cc2242580 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -4,7 +4,8 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) - 'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0': + def container_image = "/hpsuissero%3A1.0.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index 2950aa108ae..c093decc5a3 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -3,7 +3,8 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : + def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path wigs diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index f609a95ecb0..7ef4a87544b 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -4,7 +4,8 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : + def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index 6ac8771c8fb..af5b4f7028c 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -3,7 +3,8 @@ process IDR { label 'process_low' conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) - 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : + def container_image = "/idr:2.0.4.2--py39hcbe4a3b_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path peaks diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index d459557ba11..122497e1146 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -3,7 +3,8 @@ process INSTRAIN_PROFILE { label 'process_high' conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) - 'https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0': + def container_image = "/instrain:1.6.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index fa639a1f1bd..473bf5bb9b3 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -3,7 +3,8 @@ process IQTREE { label 'process_medium' conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) - 'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' : + def container_image = "/iqtree:2.1.4_beta--hdcc8f71_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index c66d95aa701..7ac02d04fe1 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -3,7 +3,8 @@ process ISMAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) - 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' : + def container_image = "/ismapper:2.0.2--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index 04279bf63ac..a55e02eee7f 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -3,7 +3,8 @@ process ISOSEQ3_CLUSTER { label 'process_medium' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : + def container_image = "/isoseq3:3.4.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index f13fbced272..033e349f5ed 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -3,7 +3,8 @@ process ISOSEQ3_REFINE { label 'process_low' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' : + def container_image = "/isoseq3:3.4.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 057f21c23c2..69b9750dc4f 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -3,7 +3,8 @@ process IVAR_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : + def container_image = "/ivar:1.3.1--h089eab3_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index 08e7a0e2dde..a75049ffeda 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -3,7 +3,8 @@ process IVAR_TRIM { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : + def container_image = "/ivar:1.3.1--h089eab3_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 42415d95fbd..2e4985d20a8 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -3,7 +3,8 @@ process IVAR_VARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' : + def container_image = "/ivar:1.3.1--h089eab3_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index 9b2bb9fa22d..fc4c2e0e977 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -8,7 +8,8 @@ process JUPYTERNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' : + def container_image = "/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index afba70a3c06..62568fdb033 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -3,7 +3,8 @@ process KAIJU_KAIJU { label 'process_high' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': + def container_image = "/kaiju:1.8.2--h5b5514e_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 6db1dab219a..e18cdaf1c27 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -3,7 +3,8 @@ process KAIJU_KAIJU2KRONA { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': + def container_image = "/kaiju:1.8.2--h5b5514e_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 451dd80d68a..83bb1d9f776 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -3,7 +3,8 @@ process KAIJU_KAIJU2TABLE { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1': + def container_image = "/kaiju:1.8.2--h5b5514e_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(results) diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index e22149fe7fb..89af4c37c94 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -3,7 +3,8 @@ process KALLISTO_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) - 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : + def container_image = "/kallisto:0.46.2--h4f7b962_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index b3f848160a8..9c564de2ab8 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -3,7 +3,8 @@ process KALLISTOBUSTOOLS_COUNT { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : + def container_image = "/kb-python:0.27.2--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 91abd06f2a6..c19bc847560 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -3,7 +3,8 @@ process KALLISTOBUSTOOLS_REF { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : + def container_image = "/kb-python:0.27.2--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 42e5b872d68..42899368f18 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -3,7 +3,8 @@ process KAT_HIST { label 'process_medium' conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) - 'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2': + def container_image = "/kat:2.4.2--py38hfc5f9d8_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index 93ba30a19b9..a9282a25187 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -3,7 +3,8 @@ process KHMER_NORMALIZEBYMEDIAN { label 'process_long' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : + def container_image = "/khmer:3.0.0a3--py37haa7609a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path pe_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 39f28e12468..3dce00235a8 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -3,7 +3,8 @@ process KHMER_UNIQUEKMERS { label 'process_low' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' : + def container_image = "/khmer:3.0.0a3--py37haa7609a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index 244512d97df..3f21fe2ac89 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -3,7 +3,8 @@ process KLEBORATE { label 'process_medium' conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) - 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' : + def container_image = "/kleborate:2.1.0--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index c4b30d43812..8d8d7d6098b 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -3,7 +3,8 @@ process KRAKEN2_KRAKEN2 { label 'process_high' conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : + def container_image = "/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index 7617f02bb1b..67ada0404c3 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,7 +2,8 @@ process KRAKENTOOLS_COMBINEKREPORTS { label 'process_single' conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': + def container_image = "/krakentools:1.2--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 588f253f8d7..f99eed84d57 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -4,7 +4,8 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - 'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0': + def container_image = "/krakentools:1.2--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index e03aa6d57e3..18e0cc3fc67 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -4,7 +4,8 @@ process KRONA_KRONADB { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : + def container_image = "/krona:2.7.1--pl526_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index a1a3ac1c96f..35320a35420 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -4,7 +4,8 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) - 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' : + def container_image = "/krona:2.8--pl5262hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 1acde0bcd6c..82f14e80c0d 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -3,7 +3,8 @@ process KRONA_KTIMPORTTEXT { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) - 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': + def container_image = "/krona:2.8.1--pl5321hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index bbc19cbe2fe..4d28c3f69ed 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -4,7 +4,8 @@ process KRONA_KTUPDATETAXONOMY { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : + def container_image = "/krona:2.7.1--pl526_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index dccad1ae27b..926f98bf717 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -3,7 +3,8 @@ process LAST_DOTPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 6cc87e06ae2..9d8a7ec43db 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -3,7 +3,8 @@ process LAST_LASTAL { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 05f4498930a..d78c98b59d4 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -3,7 +3,8 @@ process LAST_LASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index fc5a22203e9..e5343edb2d8 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -3,7 +3,8 @@ process LAST_MAFCONVERT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 771ac16e716..1154bbef0fe 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -3,7 +3,8 @@ process LAST_MAFSWAP { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 9ba02d57294..4eb6bd8ed0c 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -3,7 +3,8 @@ process LAST_POSTMASK { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 14ddaa899c0..2320715a08d 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -3,7 +3,8 @@ process LAST_SPLIT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index e08dae12deb..5ba733380df 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -3,7 +3,8 @@ process LAST_TRAIN { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' : + def container_image = "/last:1250--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index ae54135ed3f..61555c08a15 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -4,7 +4,8 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) - 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' : + def container_image = "/leehom:1.2.15--h29e30f7_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index 8d99ae20d9b..f6bf3c5e97c 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -3,7 +3,8 @@ process LEGSTA { label 'process_medium' conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) - 'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2': + def container_image = "/legsta%3A0.5.1--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 520f9ba655c..38be6fd3b72 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -3,7 +3,8 @@ process LIMA { label 'process_low' conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) - 'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' : + def container_image = "/lima:2.2.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ccs) diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index 7dc87bdc48b..eba913f814d 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -3,7 +3,8 @@ process LISSERO { label 'process_low' conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) - 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0' : + def container_image = "/lissero:0.4.9--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index d14722219a6..920be422f3e 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -3,7 +3,8 @@ process LOFREQ_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index deff438ce96..9240bb2558a 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -3,7 +3,8 @@ process LOFREQ_CALLPARALLEL { label 'process_high' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index 4ef17253c19..382033ff247 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -3,7 +3,8 @@ process LOFREQ_FILTER { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 55cd7597854..4103cc5984f 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -3,7 +3,8 @@ process LOFREQ_INDELQUAL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' : + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 2365e406054..2cfb7eb0498 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -3,7 +3,8 @@ process MACREL_CONTIGS { label 'process_medium' conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) - 'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0': + def container_image = "/macrel:1.1.0--py36hc5360cc_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index f37d75abf86..4d1353a65ea 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -3,7 +3,8 @@ process MACS2_CALLPEAK { label 'process_medium' conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) - 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' : + def container_image = "/macs2:2.2.7.1--py38h4a8c8d9_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 53c65c56d75..5bf73ad841c 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -3,7 +3,8 @@ process MAFFT { label 'process_high' conda (params.enable_conda ? "bioconda::mafft=7.490" : null) - 'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0': + def container_image = "/mafft:7.490--h779adbc_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 2dbbc35e4d6..2b83bdcbf79 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -3,7 +3,8 @@ process MALT_BUILD { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : + def container_image = "/malt:0.41--1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fastas diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index cd00e91a1df..a90e7cdc350 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -3,7 +3,8 @@ process MALT_RUN { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - 'https://depot.galaxyproject.org/singularity/malt:0.41--1' : + def container_image = "/malt:0.41--1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastqs) diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index c7cca372cd9..ac5ff48acb3 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -3,7 +3,8 @@ process MALTEXTRACT { label 'process_medium' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' : + def container_image = "/hops:0.35--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path rma6 diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 6bb07c5767d..5e627a7b55b 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -3,7 +3,8 @@ process MANTA_CONVERTINVERSION { label 'process_low' conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0': + def container_image = "/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 348fd201e82..e0f9061fc9b 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -3,7 +3,8 @@ process MANTA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : + def container_image = "/manta:1.6.0--h9ee0642_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index e67b3a1082e..023071942e5 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -3,7 +3,8 @@ process MANTA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : + def container_image = "/manta:1.6.0--h9ee0642_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index cc90cbbc14f..f0f671c09a7 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -3,7 +3,8 @@ process MANTA_TUMORONLY { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : + def container_image = "/manta:1.6.0--h9ee0642_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index e650118d99a..68a7364a470 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -3,7 +3,8 @@ process MAPDAMAGE2 { label 'process_single' conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) - 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' : + def container_image = "/mapdamage2:2.2.1--pyr40_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index f999fe8cfe8..f5abbc5459f 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -3,7 +3,8 @@ process MASH_DIST { label 'process_low' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : + def container_image = "/mash:2.3--he348c14_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 95dd1d8d1b9..083c39ae74e 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -3,7 +3,8 @@ process MASH_SCREEN { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1': + def container_image = "/mash:2.3--he348c14_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 3cb05ccea04..6f7fb55c4c7 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -2,7 +2,8 @@ process MASH_SKETCH { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' : + def container_image = "/mash:2.3--he348c14_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index e42bb667873..abdf86fca88 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -3,7 +3,8 @@ process MASHTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) - 'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' : + def container_image = "/mashtree:1.2.0--pl526h516909a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 204b989d7ff..959007debf7 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -3,7 +3,8 @@ process MAXBIN2 { label 'process_medium' conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) - 'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' : + def container_image = "/maxbin2:2.2.7--he1b5a44_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index 44e62592a1b..012622008c6 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -4,7 +4,8 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) - 'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0': + def container_image = "/mcroni%3A1.0.4--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index c4a89fae71e..0de119170ea 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -3,7 +3,8 @@ process MD5SUM { label 'process_single' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + def container_image = "/ubuntu:20.04" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index 9fbb9608c01..f844450c1b9 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -3,7 +3,8 @@ process MEDAKA { label 'process_high' conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) - 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' : + def container_image = "/medaka:1.4.4--py38h130def0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index cb013fd2da4..029b6e7d399 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -3,7 +3,8 @@ process MEGAHIT { label 'process_high' conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' : + def container_image = "/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index dc4fdd44ecf..cfedbfe66ee 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -3,7 +3,8 @@ process MEGAN_DAA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': + def container_image = "/megan:6.21.7--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(daa) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 9c65128344d..ec0883e31ef 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -3,7 +3,8 @@ process MEGAN_RMA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': + def container_image = "/megan:6.21.7--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index ecc3f8147b9..b1485d42999 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -3,7 +3,8 @@ process MENINGOTYPE { label 'process_low' conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) - 'https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0' : + def container_image = "/meningotype:0.8.5--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index 196ce99a7e8..dffe9aa4ef0 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -3,7 +3,8 @@ process MERQURY { label 'process_low' conda (params.enable_conda ? "bioconda::merqury=1.3" : null) - 'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1': + def container_image = "/merqury:1.3--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index 0261588ac21..9eeaf3ca9bb 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -3,7 +3,8 @@ process MERYL_COUNT { label 'process_medium' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': + def container_image = "/meryl:1.3--h87f3376_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 7df027e3a9e..5a7409a8923 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -3,7 +3,8 @@ process MERYL_HISTOGRAM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': + def container_image = "/meryl:1.3--h87f3376_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index de44b1201a1..5fb6fc75002 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -3,7 +3,8 @@ process MERYL_UNIONSUM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': + def container_image = "/meryl:1.3--h87f3376_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index a0721192de4..e017fdf9f68 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -3,7 +3,8 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : + def container_image = "/metabat2:2.15--h986a166_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 4e76656afd9..384afd581cf 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -3,7 +3,8 @@ process METABAT2_METABAT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' : + def container_image = "/metabat2:2.15--h986a166_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index febf47b0460..40f2fd0d8b3 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,7 +2,8 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { label 'process_single' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : + def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index d428ca85b16..195528f521a 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -3,7 +3,8 @@ process METAPHLAN3_METAPHLAN3 { label 'process_high' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' : + def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index cdea4109e94..8c01f560450 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -3,7 +3,8 @@ process METHYLDACKEL_EXTRACT { label 'process_medium' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : + def container_image = "/methyldackel:0.6.0--h22771d5_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index 81587c1b97d..ad2c115a992 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -3,7 +3,8 @@ process METHYLDACKEL_MBIAS { label 'process_low' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : + def container_image = "/methyldackel:0.6.0--h22771d5_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index ce491080e7f..41bc183a9ff 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -3,7 +3,8 @@ process MINIA { label 'process_high' conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) - 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : + def container_image = "/minia:3.2.6--h9a82719_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 031e1ab167e..0556ec038af 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -3,7 +3,8 @@ process MINIASM { label 'process_high' conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) - 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' : + def container_image = "/miniasm:0.3_r179--h5bf99c6_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index d00147e88f7..97b7fefcd74 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -3,7 +3,8 @@ process MINIMAP2_ALIGN { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : + def container_image = "/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 1bd6b3fc8f4..1b78333e080 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -2,7 +2,8 @@ process MINIMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) - 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : + def container_image = "/minimap2:2.21--h5bf99c6_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 338b2f5e4d0..6344b098192 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -3,7 +3,8 @@ process MLST { label 'process_low' conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) - 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : + def container_image = "/mlst:2.19.0--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index 9f5e52bb40c..cef68878fee 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -3,7 +3,8 @@ process MOBSUITE_RECON { label 'process_medium' conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) - 'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0': + def container_image = "/mob_suite%3A3.0.3--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 5e046b7537b..34c432bab41 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -3,7 +3,8 @@ process MOSDEPTH { label 'process_medium' conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : + def container_image = "/mosdepth:0.3.3--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index f57b3f15a13..6a6d190f084 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -2,7 +2,8 @@ process MOTUS_DOWNLOADDB { label 'process_low' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': + def container_image = "/motus:3.0.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 2dbe4c794d4..06fba27827c 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -5,7 +5,8 @@ process MOTUS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': + def container_image = "/motus:3.0.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index 941803de514..e6ddaeed3d0 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -3,7 +3,8 @@ process MOTUS_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - 'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0': + def container_image = "/motus:3.0.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index 4f4c7e09239..a976f0de653 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -3,7 +3,8 @@ process MSISENSOR_MSI { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : + def container_image = "/msisensor:0.5--hb3646a4_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index 73b6dc817b6..025f7ebe581 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -3,7 +3,8 @@ process MSISENSOR_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' : + def container_image = "/msisensor:0.5--hb3646a4_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index 3c98083220b..72269350eef 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -3,7 +3,8 @@ process MSISENSOR2_MSI { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': + def container_image = "/msisensor2:0.1--hd03093a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index 3bef5dfe42d..6c66181566e 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -3,7 +3,8 @@ process MSISENSOR2_SCAN { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - 'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0': + def container_image = "/msisensor2:0.1--hd03093a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index 1066f18c5e9..939798405cb 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -3,7 +3,8 @@ process MSISENSORPRO_MSI_SOMATIC { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : + def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index 4f5849e646a..8086bf8e09a 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -3,7 +3,8 @@ process MSISENSORPRO_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : + def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index ac937ba1ea8..5bb6ec2e204 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -3,7 +3,8 @@ process MTNUCRATIO { label 'process_single' conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) - 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' : + def container_image = "/mtnucratio:0.7--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 2a53f1b3ddd..3bb99fd66ad 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -2,7 +2,8 @@ process MULTIQC { label 'process_single' conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + def container_image = "/multiqc:1.13--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 0123d24b92f..ac345b622f3 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -3,7 +3,8 @@ process MULTIVCFANALYZER { label 'process_single' conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) - 'https://depot.galaxyproject.org/singularity/multivcfanalyzer:0.85.2--hdfd78af_1': + def container_image = "/multivcfanalyzer:0.85.2--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path vcfs diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index 459b6f035c9..f1210a0d492 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -4,7 +4,8 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : + def container_image = "/mummer:3.23--pl5262h1b792b2_12" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index dfb63b228de..247c230dd3d 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -3,7 +3,8 @@ process MUSCLE { label 'process_single' conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) - 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' : + def container_image = "/muscle:3.8.1551--h7d875b9_6" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index 59931910cfd..4f1e9349837 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -3,7 +3,8 @@ process MYKROBE_PREDICT { label 'process_low' conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) - 'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1': + def container_image = "/mykrobe:0.11.0--py39h2add14b_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 563559c0f01..1fa24ec43da 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -3,7 +3,8 @@ process NANOLYSE { label 'process_low' conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) - 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' : + def container_image = "/nanolyse:1.2.0--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index c0232ee6241..b184f01ede1 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -3,7 +3,8 @@ process NANOPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) - 'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' : + def container_image = "/nanoplot:1.40.0--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index 0af824d4161..06338c8363e 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -3,7 +3,8 @@ process NCBIGENOMEDOWNLOAD { label 'process_low' conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) - 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.1--pyh5e36f6f_0' : + def container_image = "/ncbi-genome-download:0.3.1--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val meta diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 697a257cf20..0ec1f7fe92e 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -3,7 +3,8 @@ process NEXTCLADE_DATASETGET { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : + def container_image = "/nextclade:2.2.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 54355f71bcb..751ebd74ad9 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -3,7 +3,8 @@ process NEXTCLADE_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : + def container_image = "/nextclade:2.2.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index 57221f55f23..73662d94103 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -3,7 +3,8 @@ process NEXTGENMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) - 'https://depot.galaxyproject.org/singularity/nextgenmap%3A0.5.5--hc9558a2_4' : + def container_image = "/nextgenmap%3A0.5.5--hc9558a2_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index e5669049df3..2b5c2d79979 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -3,7 +3,8 @@ process NGMASTER { label 'process_low' conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) - 'https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1' : + def container_image = "/ngmaster:0.5.8--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 04f1e7471aa..6ed78cc2d17 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,7 +2,8 @@ process NGSCHECKMATE_NCM { label 'process_low' conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) - 'https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3': + def container_image = "/ngscheckmate:1.0.0--py27r41hdfd78af_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path files diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index b4f563dc8bc..8f7a49f9de5 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -3,7 +3,8 @@ process NUCMER { label 'process_low' conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' : + def container_image = "/mummer:3.23--pl5262h1b792b2_12" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 4cc4c792d20..62baee77e38 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -3,7 +3,8 @@ process OPTITYPE { label 'process_medium' conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) - 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' : + def container_image = "/optitype:1.3.5--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index 999c7384e25..9da1cc9ba80 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -3,7 +3,8 @@ process PAIRIX { label 'process_medium' conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) - 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : + def container_image = "/pairix:0.3.7--py36h30a8e3e_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 6f6c03aa3fa..40b3cf014b8 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -3,7 +3,8 @@ process PAIRTOOLS_DEDUP { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index adccca08cad..8a85efca518 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -3,7 +3,8 @@ process PAIRTOOLS_FLIP { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index cd08c694873..8681cac60a2 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -3,7 +3,8 @@ process PAIRTOOLS_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 65863886a8f..5f2043fc083 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -3,7 +3,8 @@ process PAIRTOOLS_RESTRICT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pairs) diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index f728bac40f8..aa7b1c00533 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -3,7 +3,8 @@ process PAIRTOOLS_SELECT { label 'process_medium' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index 18211843e4c..36e40b87e03 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -3,7 +3,8 @@ process PAIRTOOLS_SORT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index 680e825716c..cbf549a4bb2 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -3,7 +3,8 @@ process PANAROO_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) - 'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0': + def container_image = "/panaroo:1.2.9--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index a240667350c..25e7a9d1068 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -3,7 +3,8 @@ process PANGOLIN { label 'process_medium' conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) - 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : + def container_image = "/pangolin:4.1.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index 679538b841b..2705b9aa12e 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -4,7 +4,8 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) - 'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' : + def container_image = "/paraclu:10--h9a82719_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 07965662e7f..bb4a29cc0c2 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -3,7 +3,8 @@ process PASTY { label 'process_single' conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) - 'https://depot.galaxyproject.org/singularity/pasty:1.0.0--hdfd78af_0': + def container_image = "/pasty:1.0.0--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index baac00835c9..6894e728b58 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -3,7 +3,8 @@ process PBBAM_PBMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) - 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' : + def container_image = "/pbbam:1.7.0--h058f120_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 1dd9336f53b..9701e9f7f42 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -3,7 +3,8 @@ process PBCCS { label 'process_low' conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) - 'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' : + def container_image = "/pbccs:6.2.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(pbi) diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 07ec5982ec2..ffdc9826b13 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -3,7 +3,8 @@ process PBPTYPER { label 'process_single' conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/pbptyper:1.0.2--hdfd78af_0': + def container_image = "/pbptyper:1.0.2--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index f9b710ccdbf..1434bcb2673 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -3,7 +3,8 @@ process PEAR { label 'process_low' conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) - 'https://depot.galaxyproject.org/singularity/pear:0.9.6--h67092d7_8': + def container_image = "/pear:0.9.6--h67092d7_8" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index f3fd2bf1de5..05be7a16081 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -3,7 +3,8 @@ process PEDDY { label 'process_low' conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) - 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : + def container_image = "/peddy:0.4.8--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index fad21cf319f..7f3b0e72fd7 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -4,7 +4,8 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) - 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' : + def container_image = "/phantompeakqualtools:1.2.2--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index e4d027057ac..b769da3c789 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -3,7 +3,8 @@ process PHYLOFLASH { label 'process_medium' conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) - 'https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1' : + def container_image = "/phyloflash:3.4--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 26bc5d26600..38386e1763f 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -3,7 +3,8 @@ process PICARD_ADDORREPLACEREADGROUPS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 0fe3850703f..73a5412bb57 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -3,7 +3,8 @@ process PICARD_CLEANSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 3778691cc53..55ca27a5024 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -3,7 +3,8 @@ process PICARD_COLLECTHSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index a0e29021da8..912882a258c 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -3,7 +3,8 @@ process PICARD_COLLECTMULTIPLEMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 3ff3947c4e2..e1bdf495811 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -3,7 +3,8 @@ process PICARD_COLLECTWGSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 568b08cfc0c..82f87de9619 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -3,7 +3,8 @@ process PICARD_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index e3d033d866f..ae9226fa65e 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -3,7 +3,8 @@ process PICARD_CROSSCHECKFINGERPRINTS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input1) diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index 2f91f0a0efc..24286f2cc60 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -3,7 +3,8 @@ process PICARD_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index 770ab0d2926..c3f0afd601e 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -3,7 +3,8 @@ process PICARD_FILTERSAMREADS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index 1b35b218f1c..bb2bdbdb647 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -3,7 +3,8 @@ process PICARD_FIXMATEINFORMATION { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index d6b2f56ebfb..504abc0c5a4 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -3,7 +3,8 @@ process PICARD_LIFTOVERVCF { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index d552ea642bf..24d98eeb6fe 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -3,7 +3,8 @@ process PICARD_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index ea27ac011bf..6d8c20ee847 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -3,7 +3,8 @@ process PICARD_MERGESAMFILES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 24ea9afe16c..4822a4646f6 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -4,7 +4,8 @@ process PICARD_RENAMESAMPLEINVCF { label 'process_single' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 6b54b3423c5..3ca2dea6fe8 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -3,7 +3,8 @@ process PICARD_SORTSAM { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 23a216593f2..d9ac24c78b6 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -3,7 +3,8 @@ process PICARD_SORTVCF { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + def container_image = "/picard:2.27.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index 14534010738..a95789f05e9 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -3,7 +3,8 @@ process PINTS_CALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) - 'https://depot.galaxyproject.org/singularity/pypints:1.1.6--pyh5e36f6f_1' : + def container_image = "/pypints:1.1.6--pyh5e36f6f_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index 37b776f1e6b..8eeae528559 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -3,7 +3,8 @@ process PIRATE { label 'process_medium' conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) - 'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' : + def container_image = "/pirate:1.0.4--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index e4de686e785..fc3836545fb 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -4,7 +4,8 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) - 'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1': + def container_image = "/plasmidfinder:2.1.6--py310hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index a2372f1dafc..fca1218ff42 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -3,7 +3,8 @@ process PLASMIDID { label 'process_medium' conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) - 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' : + def container_image = "/plasmidid:1.6.5--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index ad14cf76fda..1a07e26ee33 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -3,7 +3,8 @@ process PLINK_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : + def container_image = "/plink:1.90b6.21--h779adbc_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index 41f1fbdf731..4db6dd05ad6 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -3,7 +3,8 @@ process PLINK_VCF { label 'process_medium' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' : + def container_image = "/plink:1.90b6.21--h779adbc_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index 03c5dca69c9..131a6102951 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -3,7 +3,8 @@ process PLINK2_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : + def container_image = "/plink2:2.00a2.3--h712d239_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index a511638957d..d713330fe33 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -3,7 +3,8 @@ process PLINK2_SCORE { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : + def container_image = "/plink2:2.00a2.3--h712d239_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pgen), path(psam), path(pvar) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index c5ca87e58ec..a021613657f 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -3,7 +3,8 @@ process PLINK2_VCF { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : + def container_image = "/plink2:2.00a2.3--h712d239_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index eea916dc53d..9f30b80aace 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -3,7 +3,8 @@ process PMDTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) - 'https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5' : + def container_image = "/pmdtools:0.60--hdfd78af_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path (bai) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index 40403e1bc93..f19616720a7 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -3,7 +3,8 @@ process PORECHOP { label 'process_medium' conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) - 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : + def container_image = "/porechop:0.2.4--py39h7cff6ad_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index c7e9ce74ec4..000eb3bc283 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -4,7 +4,8 @@ process PRESEQ_CCURVE { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': + def container_image = "/preseq:3.1.2--h445547b_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 15997779de4..bcfd3ca8b51 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -4,7 +4,8 @@ process PRESEQ_LCEXTRAP { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': + def container_image = "/preseq:3.1.2--h445547b_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index 82191c4fec8..4ee07a7ad2b 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -3,7 +3,8 @@ process PRINSEQPLUSPLUS { label 'process_low' conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) - 'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1': + def container_image = "/prinseq-plus-plus:1.2.3--hc90279e_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 4af4f090ddc..8a44b7caded 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -3,7 +3,8 @@ process PRODIGAL { label 'process_single' conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : + def container_image = "/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 942eb8ec80c..2291cb3e282 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -3,7 +3,8 @@ process PROKKA { label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) - 'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' : + def container_image = "/prokka%3A1.14.6--pl5321hdfd78af_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index 92a6abed213..ad1d050de10 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -3,7 +3,8 @@ process PYCOQC { label 'process_medium' conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) - 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' : + def container_image = "/pycoqc:2.5.2--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index 3367f196ac5..87755d80993 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -3,7 +3,8 @@ process PYDAMAGE_ANALYZE { label 'process_medium' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : + def container_image = "/pydamage:0.70--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index bcc57edd0f1..ca9b67ecf9e 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -3,7 +3,8 @@ process PYDAMAGE_FILTER { label 'process_single' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : + def container_image = "/pydamage:0.70--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 3252097f751..125f8fc4488 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -3,7 +3,8 @@ process QCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) - 'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' : + def container_image = "/qcat:1.1.0--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 4747efb2688..3c28c8c1b8d 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -3,7 +3,8 @@ process QUALIMAP_BAMQC { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : + def container_image = "/qualimap:2.2.2d--1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 837a4e14de7..1a527bed414 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -3,7 +3,8 @@ process QUALIMAP_BAMQCCRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' : + def container_image = "/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cram), path(crai) diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index f0e064a1ad5..b783c66991a 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -3,7 +3,8 @@ process QUALIMAP_RNASEQ { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : + def container_image = "/qualimap:2.2.2d--1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index ffa3d2c0f88..35139a2b2bb 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -2,7 +2,8 @@ process QUAST { label 'process_medium' conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) - 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : + def container_image = "/quast:5.2.0--py39pl5321h2add14b_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path consensus diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index 58273e6c5f0..f6fd985feca 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -3,7 +3,8 @@ process RACON { label 'process_high' conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) - 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' : + def container_image = "/racon:1.4.20--h9a82719_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 9ca902b9848..8513c29eaaa 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -3,7 +3,8 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : + def container_image = "/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 03bdad2f15e..79a015f06c9 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -3,7 +3,8 @@ process RASUSA { label 'process_low' conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) - 'https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1' : + def container_image = "/rasusa:0.3.0--h779adbc_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), val(genome_size) diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index 8abf363c0d1..788dfb3226f 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -3,7 +3,8 @@ process RAVEN { label 'process_medium' conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) - 'https://depot.galaxyproject.org/singularity/raven-assembler:1.6.1--h2e03b76_0' : + def container_image = "/raven-assembler:1.6.1--h2e03b76_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index 48f4d67bbda..4ea5ad556f8 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -2,7 +2,8 @@ process RAXMLNG { label 'process_high' conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) - 'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' : + def container_image = "/raxml-ng:1.0.3--h32fcf60_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 5aa7a7a5576..467c875f0ac 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -3,7 +3,8 @@ process RGI_MAIN { label 'process_medium' conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) - 'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2': + def container_image = "/rgi:5.2.1--pyha8f3691_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index af6baaad4d0..596e6bca22e 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -3,7 +3,8 @@ process RHOCALL_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) - 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': + def container_image = "/rhocall:0.5.1--py39hbf8eff0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index e2e543dcb20..da6fa88bd94 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -8,7 +8,8 @@ process RMARKDOWNNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : + def container_image = "/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index 6789d641aa5..6dd473c5b9b 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -3,7 +3,8 @@ process ROARY { label 'process_medium' conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) - 'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' : + def container_image = "/roary:3.13.0--pl526h516909a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 430144a5aef..6e21a6fa3d2 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -3,7 +3,8 @@ process RSEM_CALCULATEEXPRESSION { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : + def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 39a68f28e45..18e84bfc76c 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -3,7 +3,8 @@ process RSEM_PREPAREREFERENCE { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' : + def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "rsem/*" diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index b88594f534e..67219602172 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -3,7 +3,8 @@ process RSEQC_BAMSTAT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index 786ea64d7c9..c434d67f86a 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -3,7 +3,8 @@ process RSEQC_INFEREXPERIMENT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index 7dcabeb19e7..e6322737868 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -3,7 +3,8 @@ process RSEQC_INNERDISTANCE { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index db1725796f4..96ef7827a50 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -3,7 +3,8 @@ process RSEQC_JUNCTIONANNOTATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index ebd549fc8cb..07041cdc19c 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -3,7 +3,8 @@ process RSEQC_JUNCTIONSATURATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index ca249e5e7f1..701f9343aac 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -3,7 +3,8 @@ process RSEQC_READDISTRIBUTION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 81dad498c47..055e6695983 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -3,7 +3,8 @@ process RSEQC_READDUPLICATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 4fb43a464a4..4b286d1b908 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -3,7 +3,8 @@ process RSEQC_TIN { label 'process_high' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : + def container_image = "/rseqc:3.0.1--py37h516909a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 57f3d9652d3..52bbb6e0573 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -3,7 +3,8 @@ process RTGTOOLS_PEDFILTER { label 'process_low' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': + def container_image = "/rtg-tools:3.12.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index d3119d9fc73..d6ee5576070 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -3,7 +3,8 @@ process RTGTOOLS_VCFEVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': + def container_image = "/rtg-tools:3.12.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index ee94cb210a6..c8292099e4d 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -3,7 +3,8 @@ process SALMON_INDEX { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : + def container_image = "/salmon:1.5.2--h84f40af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path genome_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index e145fcd0da0..7e867c806b0 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -3,7 +3,8 @@ process SALMON_QUANT { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' : + def container_image = "/salmon:1.5.2--h84f40af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index e25cc136947..3e1a7c52d6b 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -3,7 +3,8 @@ process SAMBLASTER { label 'process_low' conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' : + def container_image = "/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 01434418a3e..454289fa14f 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_AMPLICONCLIP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index 21f90de13c9..c0ca12b9bac 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_BAM2FQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 8ec1c0b8014..261629b41f1 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_COLLATE { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 7cda5b46168..887734e6065 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_COLLATEFASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index b8d733c6348..b27c0475e2b 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 6fa7c892a99..91b45defba8 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_DEPTH { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 8903cb254ca..304600d122f 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_DICT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 506d890c8e4..bd19f7a4acc 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_FAIDX { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 433ab3fcfcf..6cc3e380243 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_FASTA { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index be222d39ca3..2fe687462c5 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_FASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 3cc6045a0cb..481ca22e3b1 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_FIXMATE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b80e6cb05a7..972772d4af3 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_FLAGSTAT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index ab9b668b447..18163e13d77 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_GETRG { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index e8f3c8b6921..034eb4a2e49 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_IDXSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8f987d455fb..be48bc0acfa 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index eede1fb6df0..b9c4cfb6c5a 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_MARKDUP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0': + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 96870460947..8cd2247c305 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index 1e91e69fbef..ba5542a41ee 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_MPILEUP { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index bb3642efe33..dd78f242b93 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index fe9a8e7acc8..88d912c397e 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index c07dcefaf38..81ada981f9e 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -3,7 +3,8 @@ process SAMTOOLS_VIEW { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : + def container_image = "/samtools:1.15.1--h1170115_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index 9fc0840f7ba..df08efc136d 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -3,7 +3,8 @@ process SCOARY { label 'process_low' conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) - 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' : + def container_image = "/scoary:1.6.16--py_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index 8f6ac9ae359..4a874a738a8 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -3,7 +3,8 @@ process SCRAMBLE_CLUSTERANALYSIS { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': + def container_image = "/scramble:1.0.1--h779adbc_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(clusters) diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 5744350e614..9c30ea89b20 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -3,7 +3,8 @@ process SCRAMBLE_CLUSTERIDENTIFIER { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - 'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1': + def container_image = "/scramble:1.0.1--h779adbc_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index deccbcec971..f81d7bff98d 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -4,7 +4,8 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' : + def container_image = "/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 653388edc1d..f8d1942d68e 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -3,7 +3,8 @@ process SEQKIT_PAIR { label 'process_medium' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': + def container_image = "/seqkit:2.1.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index 7c934f9ff42..7672deb33ae 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -3,7 +3,8 @@ process SEQKIT_REPLACE { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': + def container_image = "/seqkit:2.1.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index c7b275a2a5e..0f97d32400e 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -3,7 +3,8 @@ process SEQKIT_SPLIT2 { label 'process_medium' conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) - 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : + def container_image = "/seqkit:2.1.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index 5e683226971..a2e83e68b39 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -3,7 +3,8 @@ process SEQKIT_STATS { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) - 'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0': + def container_image = "/seqkit:2.2.0--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index 77658ac9afb..e8c8d7bc153 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -3,7 +3,8 @@ process SEQSERO2 { label 'process_low' conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) - 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : + def container_image = "/seqsero2:1.2.1--py_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 44008c3668c..7a21f267ffa 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -3,7 +3,8 @@ process SEQTK_MERGEPE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + def container_image = "/seqtk:1.3--h5bf99c6_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index e3dbbd1e3a0..ed852c75b24 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -3,7 +3,8 @@ process SEQTK_RENAME { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + def container_image = "/seqtk:1.3--h5bf99c6_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index 9a0beb30fbf..e6036501713 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -3,7 +3,8 @@ process SEQTK_SAMPLE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + def container_image = "/seqtk:1.3--h5bf99c6_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index e66b00ff274..307bf12204d 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -3,7 +3,8 @@ process SEQTK_SEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + def container_image = "/seqtk:1.3--h5bf99c6_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index cdaba9a1206..829aefaac33 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -3,7 +3,8 @@ process SEQTK_SUBSEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + def container_image = "/seqtk:1.3--h5bf99c6_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path sequences diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index 77443f46386..368c9612173 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -3,7 +3,8 @@ process SEQUENZAUTILS_BAM2SEQZ { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : + def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normalbam), path(tumourbam) diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index f9fd1251d1e..070fa9e5ade 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -3,7 +3,8 @@ process SEQUENZAUTILS_GCWIGGLE { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : + def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 992a50dd259..7a906954d7a 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -4,7 +4,8 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) - 'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' : + def container_image = "/seqwish:0.7.6--h5b5514e_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index df5d5d8aed3..4fe940491d5 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -3,7 +3,8 @@ process SEROBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1': + def container_image = "/seroba:1.0.2--pyhdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index 737f95901fb..d50906a28de 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -3,7 +3,8 @@ process SEXDETERRMINE { label 'process_single' conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) - 'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1': + def container_image = "/sexdeterrmine:1.1.2--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(depth) diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 50507e92619..0667eed6260 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -3,7 +3,8 @@ process SHASTA { label 'process_medium' conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) - 'https://depot.galaxyproject.org/singularity/shasta:0.8.0--h7d875b9_0': + def container_image = "/shasta:0.8.0--h7d875b9_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index f9db7b28bcd..e330077d27a 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -3,7 +3,8 @@ process SHASUM { label 'process_low' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + def container_image = "/ubuntu:20.04" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index fa25933e75c..8f531253cd3 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -3,7 +3,8 @@ process SHIGATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) - 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0': + def container_image = "/shigatyper%3A2.0.1--pyhdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 75409487121..60ab0f21eb9 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -3,7 +3,8 @@ process SHOVILL { label 'process_medium' conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) - 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' : + def container_image = "/shovill:1.1.0--0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index f1aa8cd1f34..09655f019a3 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -3,7 +3,8 @@ process SISTR { label 'process_medium' conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) - 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2': + def container_image = "/sistr_cmd:1.1.1--pyh864c0ab_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 97ba56597e7..45a8cbee0ea 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -4,7 +4,8 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) - 'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2': + def container_image = "/slimfastq:2.04--h87f3376_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index bf0486d7a96..27955baf1a5 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -3,7 +3,8 @@ process SNAPALIGNER_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': + def container_image = "/snap-aligner:2.0.1--hd03093a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index 8fd91112614..1b799179c4c 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -3,7 +3,8 @@ process SNAPALIGNER_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - 'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1': + def container_image = "/snap-aligner:2.0.1--hd03093a_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index c3971e18746..b0596591f40 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -3,7 +3,8 @@ process SNIPPY_CORE { label 'process_medium' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2': + def container_image = "/snippy:4.6.0--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index 5b3c02c898d..eebe1257b90 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -3,7 +3,8 @@ process SNIPPY_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - 'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' : + def container_image = "/snippy:4.6.0--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 68b41edafd8..689161224ca 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -3,7 +3,8 @@ process SNPDISTS { label 'process_low' conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) - 'https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0' : + def container_image = "/snp-dists:0.8.2--h5bf99c6_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 5fb008a23d0..56bfc4f1f08 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -3,7 +3,8 @@ process SNPEFF { label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) - 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : + def container_image = "/snpeff:5.1--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index 6ca51ccb286..57c28a9eb25 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -3,7 +3,8 @@ process SNPSIFT_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) - 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : + def container_image = "/snpsift:4.3.1t--hdfd78af_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index fce03657c3f..4713a43ec28 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -2,7 +2,8 @@ process SNPSITES { label 'process_medium' conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) - 'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' : + def container_image = "/snp-sites:2.5.1--hed695b0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 377240094b4..3b5d90b41e9 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -4,7 +4,8 @@ process SOMALIER_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': + def container_image = "/somalier:0.2.15--h37c5b7d_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index 5c915c63c8c..03da2d04b9b 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -4,7 +4,8 @@ process SOMALIER_RELATE { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': + def container_image = "/somalier:0.2.15--h37c5b7d_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(extract) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index cefdfe62664..f0a2976a530 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,7 +3,8 @@ process SORTMERNA { label "process_high" conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) - 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' : + def container_image = "/sortmerna:4.3.4--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index 5f7c23d3669..64d08edaa36 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -3,7 +3,8 @@ process SOURMASH_SKETCH { label 'process_low' conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) - 'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0': + def container_image = "/sourmash:4.2.4--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 9f9002c4d94..11285ac5bb8 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -3,7 +3,8 @@ process SPADES { label 'process_high' conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) - 'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' : + def container_image = "/spades:3.15.4--h95f258a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index cd027ebd43a..887c12bc75a 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -3,7 +3,8 @@ process SPATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) - 'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' : + def container_image = "/spatyper:0.3.3--pyhdfd78af_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index c9eabb9a924..53b2934f48d 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -3,7 +3,8 @@ process SRATOOLS_FASTERQDUMP { label 'process_medium' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : + def container_image = "/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 0bcb618ff51..840ff37cc43 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -3,7 +3,8 @@ process SRATOOLS_PREFETCH { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' : + def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(id) diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 7e99aa8ede6..e90a4c8fbe6 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -3,7 +3,8 @@ process SRST2_SRST2 { label 'process_low' conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) - 'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2': + def container_image = "/srst2%3A0.2.0--py27_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 6f934256b08..d51c0770f9b 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -4,7 +4,8 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) - 'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0': + def container_image = "/ssuissero%3A1.0.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index 8dd91080941..a7a37d34a96 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -3,7 +3,8 @@ process STADENIOLIB_SCRAMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) - 'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' : + def container_image = "/staden_io_lib:1.14.14--h0d9da7e_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index 3baecab3049..3508f21e7e3 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -3,7 +3,8 @@ process STAPHOPIASCCMEC { label 'process_low' conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) - 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' : + def container_image = "/staphopia-sccmec:1.0.0--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 72a74b7fbd8..bd176f83b3e 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,7 +3,8 @@ process STAR_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : + def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index c271711dda3..27d734cff23 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,7 +3,8 @@ process STAR_GENOMEGENERATE { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : + def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 4e8f29113a2..73643112452 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -3,7 +3,8 @@ process STRANGER { label 'process_low' conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) - 'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0': + def container_image = "/stranger:0.8.1--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 3c3c798c553..23b59638ed6 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -3,7 +3,8 @@ process STRELKA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : + def container_image = "/strelka:2.9.10--h9ee0642_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 055350daba9..8bd62b9bb35 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -3,7 +3,8 @@ process STRELKA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : + def container_image = "/strelka:2.9.10--h9ee0642_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 3641a3a26c3..9fab02f01d7 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -3,7 +3,8 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : + def container_image = "/stringtie:2.2.1--hecb563c_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 31f7d30f307..eebde511543 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -3,7 +3,8 @@ process STRINGTIE_STRINGTIE { label 'process_medium' conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : + def container_image = "/stringtie:2.2.1--hecb563c_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 9b657b2993e..443aa0edb5c 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -3,7 +3,8 @@ process SUBREAD_FEATURECOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) - 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : + def container_image = "/subread:2.0.1--hed695b0_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index f6e2c7d68a9..fb12c07079f 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -2,7 +2,8 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0': + def container_image = "/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 52461e9ef9b..3be936d62c2 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -3,7 +3,8 @@ process SVDB_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0': + def container_image = "/svdb:2.6.1--py39h5371cbf_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index 8e12272cdd4..804c4a91bf4 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -3,7 +3,8 @@ process SVTK_STANDARDIZE { label 'process_low' conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) - 'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2': + def container_image = "/svtk:0.0.20190615--py37h73a75cf_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 4dbb8898d94..0e7f67bcad3 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -3,7 +3,8 @@ process TABIX_BGZIPTABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : + def container_image = "/tabix:1.11--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 87b6d7937e4..b1eb6e1637a 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -3,7 +3,8 @@ process TABIX_TABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : + def container_image = "/tabix:1.11--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 55c42b333f1..69c1ff27684 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -3,7 +3,8 @@ process TAILFINDR { label 'process_high' conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0': + def container_image = "/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index 89f8531c607..9dc73d53f9c 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -3,7 +3,8 @@ process TBPROFILER_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) - 'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' : + def container_image = "/tb-profiler:3.0.8--pypyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index c91baa77085..7b5f912061b 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -3,7 +3,8 @@ process TIDDIT_COV { label 'process_low' conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) - 'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' : + def container_image = "/tiddit:3.0.0--py39h59fae87_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index d40f2e83d73..9082419dfec 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -3,7 +3,8 @@ process TIDDIT_SV { label 'process_medium' conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) - 'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' : + def container_image = "/tiddit:3.1.0--py39h59fae87_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index ad638b46d93..efaa44a9a3e 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -3,7 +3,8 @@ process TRANSDECODER_LONGORF { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4' : + def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'quay.io/comp-bio-aging/transdecoder' }" input: diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index 2a56809ee02..266028d887f 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -3,7 +3,8 @@ process TRANSDECODER_PREDICT { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4': + def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'quay.io/comp-bio-aging/transdecoder' }" input: diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 8c86e2c1b53..3a532e02968 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -3,7 +3,8 @@ process TRIMGALORE { label 'process_high' conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : + def container_image = "/trim-galore:0.6.7--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 966c18a2cd9..a1a72803aa0 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -3,7 +3,8 @@ process TRIMMOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) - 'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2': + def container_image = "/trimmomatic:0.39--hdfd78af_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index 9e3ffe278e4..af547be54ab 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -4,7 +4,8 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) - 'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' : + def container_image = "/ucsc-bedclip:377--h0b8a92a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 473bf7e411c..f5e04c36204 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -4,7 +4,8 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) - 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' : + def container_image = "/ucsc-bedgraphtobigwig:377--h446ed27_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index d7a8439845c..9d8a09a952b 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -4,7 +4,8 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) - 'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--ha8a8165_3' : + def container_image = "/ucsc-bedtobigbed:377--ha8a8165_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index 7527efa52ab..749d7ae1c1b 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -4,7 +4,8 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) - 'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' : + def container_image = "/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index 8904e20ee1b..e7b650c8471 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -4,7 +4,8 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) - 'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' : + def container_image = "/ucsc-liftover:377--h0b8a92a_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 59db9a260ef..c87602b7aac 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -4,7 +4,8 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) - 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' : + def container_image = "/ucsc-wigtobigwig:377--h0b8a92a_2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index d0e8db4bf93..d332bb6a4e7 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -3,7 +3,8 @@ process ULTRA_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0': + def container_image = "/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 9750810cb18..6801d6e36d6 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -3,7 +3,8 @@ process ULTRA_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) - 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0': + def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index c13fe9e1ed8..65a02ad0ae6 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -3,7 +3,8 @@ process ULTRA_PIPELINE { label 'process_high' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) - 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' : + def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 0fcfecd13de..716ab3a2a7a 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -3,7 +3,8 @@ process UMITOOLS_DEDUP { label "process_medium" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : + def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 9df3c875af4..20286880cc3 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -3,7 +3,8 @@ process UMITOOLS_EXTRACT { label "process_low" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : + def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index e0c049daf6e..a61e75b0e99 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -3,7 +3,8 @@ process UNICYCLER { label 'process_high' conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) - 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : + def container_image = "/unicycler:0.4.8--py38h8162308_3" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 3e018d73dfa..73bacd4d5d2 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -3,7 +3,8 @@ process UNTAR { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + def container_image = "/ubuntu:20.04" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 088a0b62a86..401e0f6bd5e 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -3,7 +3,8 @@ process UNZIP { label 'process_single' conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) - 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' : + def container_image = "/p7zip:15.09--h2d50403_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 0dbaa9a271e..90f9e609547 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -3,7 +3,8 @@ process VARDICTJAVA { label 'process_medium' conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) - 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': + def container_image = "/vardict-java:1.8.3--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 1a6699e8231..f02ebb6b42d 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -4,7 +4,8 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) - 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' : + def container_image = "/variantbam:1.4.4a--h7d7f7ad_5" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index f0d1627de69..5cd5613f08e 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,7 +4,8 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) - 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1': + def container_image = "/vcf2db:2020.02.24--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 4bb420db090..098b9f00d1c 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -5,7 +5,8 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0': + def container_image = "/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index b1c576cb48f..dd55cb39ff7 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -3,7 +3,8 @@ process VCFANNO { label 'process_low' conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) - 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': + def container_image = "/vcfanno:0.3.3--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 2fba356867a..8e7b5b93d04 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -3,7 +3,8 @@ process VCFLIB_VCFBREAKMULTI { label 'process_low' conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': + def container_image = "/vcflib:1.0.3--hecb563c_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index d1094f44d0a..b620a759376 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -4,7 +4,8 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': + def container_image = "/vcflib:1.0.3--hecb563c_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index 8b85f72ce88..ff0b12ac1be 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -3,7 +3,8 @@ process VCFTOOLS { label 'process_single' conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) - 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' : + def container_image = "/vcftools:0.1.16--he513fc3_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 4deb7c70e4f..07edd9543b2 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,7 +3,8 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) - 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : + def container_image = "/verifybamid2:2.0.1--hbb20b25_6" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 4470995414f..a11cfa380ab 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -3,7 +3,8 @@ process VSEARCH_SINTAX { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': + def container_image = "/vsearch:2.21.1--h95f258a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index bebc2ed57c8..67411a81a9f 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -3,7 +3,8 @@ process VSEARCH_USEARCHGLOBAL { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': + def container_image = "/vsearch:2.21.1--h95f258a_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index 22f46050b6e..e122c5db66e 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -3,7 +3,8 @@ process WGSIM { label 'process_medium' conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) - 'https://depot.galaxyproject.org/singularity/wgsim:1.0--h5bf99c6_4': + def container_image = "/wgsim:1.0--h5bf99c6_4" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index dd2d75b9e80..f618397a612 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -3,7 +3,8 @@ process WHAMG { label 'process_medium' conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) - 'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1': + def container_image = "/wham:1.8.0.1.2017.05.03--h8b12597_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index a8278d1d71b..1a4db5136a4 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -3,7 +3,8 @@ process YARA_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) - 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' : + def container_image = "/yara:1.0.2--2" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 7bc49412d76..ff6a0507db5 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -3,7 +3,8 @@ process YARA_MAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) - 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' : + def container_image = "/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) From 61845a0386e7467ddab2bb7e836ac4b5f7d48ef2 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 17:27:54 +0200 Subject: [PATCH 17/21] style: Fix indentation of def container_image --- modules/nf-core/abacas/main.nf | 2 +- modules/nf-core/abricate/run/main.nf | 2 +- modules/nf-core/abricate/summary/main.nf | 2 +- modules/nf-core/adapterremoval/main.nf | 2 +- modules/nf-core/adapterremovalfixprefix/main.nf | 2 +- modules/nf-core/agrvate/main.nf | 2 +- modules/nf-core/allelecounter/main.nf | 2 +- modules/nf-core/ampir/main.nf | 2 +- modules/nf-core/amplify/predict/main.nf | 2 +- modules/nf-core/amps/main.nf | 3 ++- modules/nf-core/amrfinderplus/run/main.nf | 2 +- modules/nf-core/amrfinderplus/update/main.nf | 3 ++- modules/nf-core/angsd/docounts/main.nf | 2 +- modules/nf-core/antismash/antismashlite/main.nf | 2 +- .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 2 +- modules/nf-core/aria2/main.nf | 2 +- modules/nf-core/ariba/getref/main.nf | 3 ++- modules/nf-core/ariba/run/main.nf | 3 ++- modules/nf-core/arriba/main.nf | 3 ++- modules/nf-core/artic/guppyplex/main.nf | 3 ++- modules/nf-core/artic/minion/main.nf | 2 +- modules/nf-core/ascat/main.nf | 2 +- modules/nf-core/assemblyscan/main.nf | 2 +- modules/nf-core/ataqv/ataqv/main.nf | 2 +- modules/nf-core/ataqv/mkarv/main.nf | 2 +- modules/nf-core/atlas/call/main.nf | 2 +- modules/nf-core/atlas/pmd/main.nf | 2 +- modules/nf-core/atlas/recal/main.nf | 2 +- modules/nf-core/atlas/splitmerge/main.nf | 2 +- modules/nf-core/bakta/main.nf | 2 +- modules/nf-core/bamaligncleaner/main.nf | 2 +- modules/nf-core/bamcmp/main.nf | 2 +- modules/nf-core/bamtools/convert/main.nf | 2 +- modules/nf-core/bamtools/split/main.nf | 2 +- modules/nf-core/bamtools/stats/main.nf | 2 +- modules/nf-core/bamutil/trimbam/main.nf | 2 +- modules/nf-core/bandage/image/main.nf | 2 +- modules/nf-core/bbmap/align/main.nf | 2 +- modules/nf-core/bbmap/bbduk/main.nf | 2 +- modules/nf-core/bbmap/bbsplit/main.nf | 2 +- modules/nf-core/bbmap/clumpify/main.nf | 2 +- modules/nf-core/bbmap/index/main.nf | 2 +- modules/nf-core/bbmap/pileup/main.nf | 2 +- modules/nf-core/bcftools/annotate/main.nf | 2 +- modules/nf-core/bcftools/concat/main.nf | 2 +- modules/nf-core/bcftools/consensus/main.nf | 2 +- modules/nf-core/bcftools/convert/main.nf | 2 +- modules/nf-core/bcftools/filter/main.nf | 2 +- modules/nf-core/bcftools/index/main.nf | 2 +- modules/nf-core/bcftools/isec/main.nf | 2 +- modules/nf-core/bcftools/merge/main.nf | 2 +- modules/nf-core/bcftools/mpileup/main.nf | 2 +- modules/nf-core/bcftools/norm/main.nf | 2 +- modules/nf-core/bcftools/query/main.nf | 2 +- modules/nf-core/bcftools/reheader/main.nf | 2 +- modules/nf-core/bcftools/roh/main.nf | 2 +- modules/nf-core/bcftools/sort/main.nf | 2 +- modules/nf-core/bcftools/stats/main.nf | 2 +- modules/nf-core/bcftools/view/main.nf | 2 +- modules/nf-core/bedtools/bamtobed/main.nf | 2 +- modules/nf-core/bedtools/complement/main.nf | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/bedtools/getfasta/main.nf | 2 +- modules/nf-core/bedtools/intersect/main.nf | 2 +- modules/nf-core/bedtools/makewindows/main.nf | 2 +- modules/nf-core/bedtools/maskfasta/main.nf | 2 +- modules/nf-core/bedtools/merge/main.nf | 2 +- modules/nf-core/bedtools/slop/main.nf | 2 +- modules/nf-core/bedtools/sort/main.nf | 2 +- modules/nf-core/bedtools/split/main.nf | 2 +- modules/nf-core/bedtools/subtract/main.nf | 2 +- modules/nf-core/biobambam/bammerge/main.nf | 2 +- modules/nf-core/biscuit/align/main.nf | 2 +- modules/nf-core/biscuit/biscuitblaster/main.nf | 2 +- modules/nf-core/biscuit/bsconv/main.nf | 2 +- modules/nf-core/biscuit/epiread/main.nf | 2 +- modules/nf-core/biscuit/index/main.nf | 2 +- modules/nf-core/biscuit/mergecg/main.nf | 2 +- modules/nf-core/biscuit/pileup/main.nf | 2 +- modules/nf-core/biscuit/qc/main.nf | 2 +- modules/nf-core/biscuit/vcf2bed/main.nf | 3 ++- modules/nf-core/bismark/align/main.nf | 2 +- modules/nf-core/bismark/deduplicate/main.nf | 2 +- modules/nf-core/bismark/genomepreparation/main.nf | 2 +- modules/nf-core/bismark/methylationextractor/main.nf | 2 +- modules/nf-core/bismark/report/main.nf | 2 +- modules/nf-core/bismark/summary/main.nf | 2 +- modules/nf-core/blast/blastn/main.nf | 2 +- modules/nf-core/blast/makeblastdb/main.nf | 2 +- modules/nf-core/blast/tblastn/main.nf | 2 +- modules/nf-core/bowtie/align/main.nf | 2 +- modules/nf-core/bowtie/build/main.nf | 2 +- modules/nf-core/bowtie2/build/main.nf | 2 +- modules/nf-core/bracken/bracken/main.nf | 2 +- modules/nf-core/bracken/combinebrackenoutputs/main.nf | 2 +- modules/nf-core/busco/main.nf | 3 ++- modules/nf-core/bwa/aln/main.nf | 2 +- modules/nf-core/bwa/index/main.nf | 3 ++- modules/nf-core/bwa/mem/main.nf | 3 ++- modules/nf-core/bwa/sampe/main.nf | 3 ++- modules/nf-core/bwa/samse/main.nf | 2 +- modules/nf-core/bwamem2/index/main.nf | 3 ++- modules/nf-core/bwamem2/mem/main.nf | 3 ++- modules/nf-core/bwameth/align/main.nf | 2 +- modules/nf-core/bwameth/index/main.nf | 2 +- modules/nf-core/cat/cat/main.nf | 2 +- modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/centrifuge/centrifuge/main.nf | 2 +- modules/nf-core/centrifuge/kreport/main.nf | 2 +- modules/nf-core/checkm/lineagewf/main.nf | 2 +- modules/nf-core/checkm/qa/main.nf | 2 +- modules/nf-core/chromap/chromap/main.nf | 2 +- modules/nf-core/chromap/index/main.nf | 2 +- modules/nf-core/clonalframeml/main.nf | 3 ++- modules/nf-core/cmseq/polymut/main.nf | 2 +- modules/nf-core/cnvkit/antitarget/main.nf | 2 +- modules/nf-core/cnvkit/batch/main.nf | 2 +- modules/nf-core/cnvkit/reference/main.nf | 2 +- modules/nf-core/cnvpytor/callcnvs/main.nf | 2 +- modules/nf-core/cnvpytor/histogram/main.nf | 2 +- modules/nf-core/cnvpytor/importreaddepth/main.nf | 2 +- modules/nf-core/cnvpytor/partition/main.nf | 2 +- modules/nf-core/cnvpytor/view/main.nf | 2 +- modules/nf-core/controlfreec/assesssignificance/main.nf | 2 +- modules/nf-core/controlfreec/freec/main.nf | 2 +- modules/nf-core/controlfreec/freec2bed/main.nf | 2 +- modules/nf-core/controlfreec/freec2circos/main.nf | 2 +- modules/nf-core/controlfreec/makegraph/main.nf | 2 +- modules/nf-core/cooler/cload/main.nf | 2 +- modules/nf-core/cooler/digest/main.nf | 2 +- modules/nf-core/cooler/dump/main.nf | 2 +- modules/nf-core/cooler/merge/main.nf | 2 +- modules/nf-core/cooler/zoomify/main.nf | 2 +- modules/nf-core/crumble/main.nf | 2 +- modules/nf-core/csvtk/concat/main.nf | 2 +- modules/nf-core/csvtk/split/main.nf | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/custom/getchromsizes/main.nf | 2 +- modules/nf-core/custom/sratoolsncbisettings/main.nf | 2 +- modules/nf-core/cutadapt/main.nf | 2 +- modules/nf-core/damageprofiler/main.nf | 2 +- modules/nf-core/dastool/dastool/main.nf | 3 ++- modules/nf-core/dastool/fastatocontig2bin/main.nf | 3 ++- modules/nf-core/dastool/scaffolds2bin/main.nf | 3 ++- modules/nf-core/dedup/main.nf | 4 ++-- modules/nf-core/deeparg/downloaddata/main.nf | 2 +- modules/nf-core/deeparg/predict/main.nf | 2 +- modules/nf-core/deepbgc/download/main.nf | 2 +- modules/nf-core/deepbgc/pipeline/main.nf | 2 +- modules/nf-core/deeptools/bamcoverage/main.nf | 3 ++- modules/nf-core/deeptools/computematrix/main.nf | 3 ++- modules/nf-core/deeptools/plotfingerprint/main.nf | 3 ++- modules/nf-core/deeptools/plotheatmap/main.nf | 3 ++- modules/nf-core/deeptools/plotprofile/main.nf | 3 ++- modules/nf-core/delly/call/main.nf | 2 +- 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modules/nf-core/raven/main.nf | 2 +- modules/nf-core/raxmlng/main.nf | 2 +- modules/nf-core/rgi/main/main.nf | 2 +- modules/nf-core/rhocall/annotate/main.nf | 3 ++- modules/nf-core/rmarkdownnotebook/main.nf | 2 +- modules/nf-core/roary/main.nf | 2 +- modules/nf-core/rsem/calculateexpression/main.nf | 2 +- modules/nf-core/rsem/preparereference/main.nf | 2 +- modules/nf-core/rseqc/bamstat/main.nf | 2 +- modules/nf-core/rseqc/inferexperiment/main.nf | 2 +- modules/nf-core/rseqc/innerdistance/main.nf | 2 +- modules/nf-core/rseqc/junctionannotation/main.nf | 2 +- modules/nf-core/rseqc/junctionsaturation/main.nf | 2 +- modules/nf-core/rseqc/readdistribution/main.nf | 2 +- modules/nf-core/rseqc/readduplication/main.nf | 2 +- modules/nf-core/rseqc/tin/main.nf | 2 +- modules/nf-core/rtgtools/pedfilter/main.nf | 2 +- modules/nf-core/rtgtools/vcfeval/main.nf | 2 +- modules/nf-core/salmon/index/main.nf | 2 +- modules/nf-core/salmon/quant/main.nf | 2 +- modules/nf-core/samblaster/main.nf | 2 +- modules/nf-core/samtools/ampliconclip/main.nf | 2 +- modules/nf-core/samtools/bam2fq/main.nf | 2 +- modules/nf-core/samtools/collate/main.nf | 2 +- modules/nf-core/samtools/collatefastq/main.nf | 2 +- modules/nf-core/samtools/convert/main.nf | 2 +- modules/nf-core/samtools/depth/main.nf | 2 +- modules/nf-core/samtools/dict/main.nf | 2 +- modules/nf-core/samtools/faidx/main.nf | 2 +- modules/nf-core/samtools/fasta/main.nf | 2 +- modules/nf-core/samtools/fastq/main.nf | 2 +- modules/nf-core/samtools/fixmate/main.nf | 2 +- modules/nf-core/samtools/flagstat/main.nf | 2 +- modules/nf-core/samtools/getrg/main.nf | 2 +- modules/nf-core/samtools/idxstats/main.nf | 2 +- modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/markdup/main.nf | 2 +- modules/nf-core/samtools/merge/main.nf | 2 +- modules/nf-core/samtools/mpileup/main.nf | 2 +- modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/scoary/main.nf | 3 ++- modules/nf-core/scramble/clusteranalysis/main.nf | 2 +- modules/nf-core/scramble/clusteridentifier/main.nf | 2 +- modules/nf-core/seacr/callpeak/main.nf | 2 +- modules/nf-core/seqkit/pair/main.nf | 2 +- modules/nf-core/seqkit/replace/main.nf | 2 +- modules/nf-core/seqkit/split2/main.nf | 2 +- modules/nf-core/seqkit/stats/main.nf | 2 +- modules/nf-core/seqsero2/main.nf | 2 +- modules/nf-core/seqtk/mergepe/main.nf | 2 +- modules/nf-core/seqtk/rename/main.nf | 2 +- modules/nf-core/seqtk/sample/main.nf | 2 +- modules/nf-core/seqtk/seq/main.nf | 2 +- modules/nf-core/seqtk/subseq/main.nf | 2 +- modules/nf-core/sequenzautils/bam2seqz/main.nf | 2 +- modules/nf-core/sequenzautils/gcwiggle/main.nf | 2 +- modules/nf-core/seqwish/induce/main.nf | 2 +- modules/nf-core/seroba/run/main.nf | 2 +- modules/nf-core/sexdeterrmine/main.nf | 2 +- modules/nf-core/shasta/main.nf | 2 +- modules/nf-core/shasum/main.nf | 2 +- modules/nf-core/shigatyper/main.nf | 2 +- modules/nf-core/shovill/main.nf | 2 +- modules/nf-core/sistr/main.nf | 3 ++- modules/nf-core/slimfastq/main.nf | 2 +- modules/nf-core/snapaligner/align/main.nf | 2 +- modules/nf-core/snapaligner/index/main.nf | 2 +- modules/nf-core/snippy/core/main.nf | 2 +- modules/nf-core/snippy/run/main.nf | 2 +- modules/nf-core/snpdists/main.nf | 2 +- modules/nf-core/snpeff/main.nf | 2 +- modules/nf-core/snpsift/split/main.nf | 3 ++- modules/nf-core/snpsites/main.nf | 3 ++- modules/nf-core/somalier/extract/main.nf | 2 +- modules/nf-core/somalier/relate/main.nf | 2 +- modules/nf-core/sortmerna/main.nf | 2 +- modules/nf-core/sourmash/sketch/main.nf | 2 +- modules/nf-core/spades/main.nf | 2 +- modules/nf-core/spatyper/main.nf | 2 +- modules/nf-core/sratools/fasterqdump/main.nf | 2 +- modules/nf-core/sratools/prefetch/main.nf | 2 +- modules/nf-core/srst2/srst2/main.nf | 2 +- modules/nf-core/ssuissero/main.nf | 2 +- modules/nf-core/stadeniolib/scramble/main.nf | 2 +- modules/nf-core/staphopiasccmec/main.nf | 3 ++- modules/nf-core/star/align/main.nf | 2 +- modules/nf-core/star/genomegenerate/main.nf | 2 +- modules/nf-core/stranger/main.nf | 2 +- modules/nf-core/strelka/germline/main.nf | 2 +- modules/nf-core/strelka/somatic/main.nf | 2 +- modules/nf-core/stringtie/merge/main.nf | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 3 ++- modules/nf-core/subread/featurecounts/main.nf | 3 ++- modules/nf-core/svdb/merge/main.nf | 2 +- modules/nf-core/svdb/query/main.nf | 2 +- modules/nf-core/svtk/standardize/main.nf | 2 +- modules/nf-core/tabix/bgziptabix/main.nf | 2 +- modules/nf-core/tabix/tabix/main.nf | 2 +- modules/nf-core/tailfindr/main.nf | 2 +- modules/nf-core/tbprofiler/profile/main.nf | 2 +- modules/nf-core/tiddit/cov/main.nf | 2 +- modules/nf-core/tiddit/sv/main.nf | 2 +- modules/nf-core/transdecoder/longorf/main.nf | 2 +- modules/nf-core/transdecoder/predict/main.nf | 2 +- modules/nf-core/trimgalore/main.nf | 3 ++- modules/nf-core/trimmomatic/main.nf | 2 +- modules/nf-core/ucsc/bedclip/main.nf | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 2 +- modules/nf-core/ucsc/bedtobigbed/main.nf | 2 +- modules/nf-core/ucsc/bigwigaverageoverbed/main.nf | 2 +- modules/nf-core/ucsc/liftover/main.nf | 2 +- modules/nf-core/ucsc/wigtobigwig/main.nf | 2 +- modules/nf-core/ultra/align/main.nf | 2 +- modules/nf-core/ultra/index/main.nf | 2 +- modules/nf-core/ultra/pipeline/main.nf | 2 +- modules/nf-core/umitools/dedup/main.nf | 2 +- modules/nf-core/umitools/extract/main.nf | 2 +- modules/nf-core/unicycler/main.nf | 2 +- modules/nf-core/untar/main.nf | 3 ++- modules/nf-core/unzip/main.nf | 3 ++- modules/nf-core/vardictjava/main.nf | 2 +- modules/nf-core/variantbam/main.nf | 2 +- modules/nf-core/vcf2db/main.nf | 2 +- modules/nf-core/vcf2maf/main.nf | 2 +- modules/nf-core/vcfanno/main.nf | 3 ++- modules/nf-core/vcflib/vcfbreakmulti/main.nf | 2 +- modules/nf-core/vcflib/vcfuniq/main.nf | 2 +- modules/nf-core/vcftools/main.nf | 2 +- modules/nf-core/verifybamid/verifybamid2/main.nf | 2 +- modules/nf-core/vsearch/sintax/main.nf | 2 +- modules/nf-core/vsearch/usearchglobal/main.nf | 2 +- modules/nf-core/wgsim/main.nf | 2 +- modules/nf-core/whamg/main.nf | 2 +- modules/nf-core/yara/index/main.nf | 3 ++- modules/nf-core/yara/mapper/main.nf | 3 ++- 609 files changed, 707 insertions(+), 610 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index fadddcb598f..d99ba63cdf8 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -3,7 +3,7 @@ process ABACAS { label 'process_medium' conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) - def container_image = "/abacas:1.3.1--pl526_0" + def container_image = "/abacas:1.3.1--pl526_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index ff7ef29758d..9dae4716625 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -3,7 +3,7 @@ process ABRICATE_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - def container_image = "/abricate%3A1.0.1--ha8f3691_1" + def container_image = "/abricate%3A1.0.1--ha8f3691_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index 4397ed7da67..a618ffe9f49 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -3,7 +3,7 @@ process ABRICATE_SUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - def container_image = "/abricate%3A1.0.1--ha8f3691_1" + def container_image = "/abricate%3A1.0.1--ha8f3691_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 18c86ffcb24..2119f98be10 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -3,7 +3,7 @@ process ADAPTERREMOVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) - def container_image = "/adapterremoval:2.3.2--hb7ba0dd_0" + def container_image = "/adapterremoval:2.3.2--hb7ba0dd_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index ab36fcd5622..50f4fe8d0bf 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -4,7 +4,7 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) - def container_image = "/adapterremovalfixprefix:0.0.5--hdfd78af_2" + def container_image = "/adapterremovalfixprefix:0.0.5--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 3906366cdb6..d49d010bff4 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -3,7 +3,7 @@ process AGRVATE { label 'process_low' conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) - def container_image = "/agrvate:1.0.2--hdfd78af_0" + def container_image = "/agrvate:1.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index 898f6c33c4d..0a9ea5dc3ba 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -3,7 +3,7 @@ process ALLELECOUNTER { label 'process_low' conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) - def container_image = "/cancerit-allelecount:4.3.0--h41abebc_0" + def container_image = "/cancerit-allelecount:4.3.0--h41abebc_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index 0f4011afd05..a038bce4ecf 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -3,7 +3,7 @@ process AMPIR { label 'process_single' conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) - def container_image = "/r-ampir:1.1.0" + def container_image = "/r-ampir:1.1.0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 62681feec70..c42ef6b172d 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -4,7 +4,7 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) - def container_image = "/amplify:1.0.3--py36hdfd78af_0" + def container_image = "/amplify:1.0.3--py36hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 871b1659fa9..6b084fc3ace 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -2,8 +2,9 @@ process AMPS { label 'process_low' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - def container_image = "/hops:0.35--hdfd78af_1" + def container_image = "/hops:0.35--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 4076eac9b42..63f5b0b0a0a 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -3,7 +3,7 @@ process AMRFINDERPLUS_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" + def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index e49dd098f09..27456eee12d 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -3,8 +3,9 @@ process AMRFINDERPLUS_UPDATE { label 'process_single' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" + def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index be1094d9ad0..66028a9058d 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -3,7 +3,7 @@ process ANGSD_DOCOUNTS { label 'process_low' conda (params.enable_conda ? "bioconda::angsd=0.939" : null) - def container_image = "/angsd:0.939--h468462d_0" + def container_image = "/angsd:0.939--h468462d_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index a6fe2414007..2859d6005d0 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -3,7 +3,7 @@ process ANTISMASH_ANTISMASHLITE { label 'process_medium' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" + def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } containerOptions { diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 87fdfde1c8d..d2e5c66b89a 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,7 +2,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { label 'process_single' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" + def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 6f388d491c5..41455f42199 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -4,7 +4,7 @@ process ARIA2 { label 'process_single' conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) - def container_image = "/aria2:1.36.0" + def container_image = "/aria2:1.36.0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index 754cb90239b..ab1f9d50af8 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -3,8 +3,9 @@ process ARIBA_GETREF { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - def container_image = "/ariba:2.14.6--py39h67e14b5_3" + def container_image = "/ariba:2.14.6--py39h67e14b5_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 4b34b534067..3060c8e6bad 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -3,8 +3,9 @@ process ARIBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - def container_image = "/ariba:2.14.6--py39h67e14b5_3" + def container_image = "/ariba:2.14.6--py39h67e14b5_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 394f60898f5..d826303d295 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -3,8 +3,9 @@ process ARRIBA { label 'process_medium' conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) - def container_image = "/arriba:2.3.0--haa8aa89_0" + def container_image = "/arriba:2.3.0--haa8aa89_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 79c4a678f46..410fba484c6 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -3,8 +3,9 @@ process ARTIC_GUPPYPLEX { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - def container_image = "/artic:1.2.2--pyhdfd78af_0" + def container_image = "/artic:1.2.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index dc121130bc8..cad99f79409 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -3,7 +3,7 @@ process ARTIC_MINION { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - def container_image = "/artic:1.2.2--pyhdfd78af_0" + def container_image = "/artic:1.2.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index dc514cd0974..973f286d40e 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -3,7 +3,7 @@ process ASCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) - def container_image = "/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" + def container_image = "/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 2078c9504e6..23baf502ee2 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -3,7 +3,7 @@ process ASSEMBLYSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) - def container_image = "/assembly-scan:0.4.1--pyhdfd78af_0" + def container_image = "/assembly-scan:0.4.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index cfb609a3248..55ae0be671b 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -3,7 +3,7 @@ process ATAQV_ATAQV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - def container_image = "/ataqv:1.3.0--py39hccc85d7_2" + def container_image = "/ataqv:1.3.0--py39hccc85d7_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index c99214d747c..4b9ef598bf0 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -2,7 +2,7 @@ process ATAQV_MKARV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - def container_image = "/ataqv:1.3.0--py39hccc85d7_2" + def container_image = "/ataqv:1.3.0--py39hccc85d7_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 56e6b4dbfc8..05a53341b99 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -3,7 +3,7 @@ process ATLAS_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" + def container_image = "/atlas:0.9.9--h082e891_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index 7ba87526473..cbbba2b4733 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -3,7 +3,7 @@ process ATLAS_PMD { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" + def container_image = "/atlas:0.9.9--h082e891_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index 52666da07f1..e5d42fbcbca 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -3,7 +3,7 @@ process ATLAS_RECAL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" + def container_image = "/atlas:0.9.9--h082e891_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index 06f01705c2a..8ebe9785a38 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -3,7 +3,7 @@ process ATLAS_SPLITMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" + def container_image = "/atlas:0.9.9--h082e891_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index 8daf7f458ae..c29f6548727 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -3,7 +3,7 @@ process BAKTA { label 'process_medium' conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) - def container_image = "/bakta:1.5.0--pyhdfd78af_0" + def container_image = "/bakta:1.5.0--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index 85cc97402c5..154444f207c 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -3,7 +3,7 @@ process BAMALIGNCLEANER { label 'process_low' conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) - def container_image = "/bamaligncleaner:0.2.1--pyhdfd78af_0" + def container_image = "/bamaligncleaner:0.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index bcdff49de8b..3b8863800cf 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -3,7 +3,7 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) - def container_image = "/bamcmp:2.2--h05f6578_0" + def container_image = "/bamcmp:2.2--h05f6578_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index 6a5e5f588a9..c8c3b561538 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -3,7 +3,7 @@ process BAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - def container_image = "/bamtools:2.5.1--h9a82719_9" + def container_image = "/bamtools:2.5.1--h9a82719_9" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index 33496c6ecf2..ca3cdfb3bdb 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -3,7 +3,7 @@ process BAMTOOLS_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) - def container_image = "/bamtools:2.5.2--hd03093a_0" + def container_image = "/bamtools:2.5.2--hd03093a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index e52fe198d27..4d82b8f50ae 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -3,7 +3,7 @@ process BAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - def container_image = "/bamtools:2.5.1--h9a82719_9" + def container_image = "/bamtools:2.5.1--h9a82719_9" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 16bf907c4a0..13e72741cd8 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -3,7 +3,7 @@ process BAMUTIL_TRIMBAM { label 'process_single' conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) - def container_image = "/bamutil:1.0.15--h2e03b76_1" + def container_image = "/bamutil:1.0.15--h2e03b76_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 6a0e748a79d..3550e57b711 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -3,7 +3,7 @@ process BANDAGE_IMAGE { label 'process_low' conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) - def container_image = "/bandage:0.8.1--hc9558a2_2" + def container_image = "/bandage:0.8.1--hc9558a2_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 652b0694584..9adb38b4405 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -3,7 +3,7 @@ process BBMAP_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" + def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 778d5f4e09d..b10ff1a0999 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -3,7 +3,7 @@ process BBMAP_BBDUK { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) - def container_image = "/bbmap:38.90--he522d1c_1" + def container_image = "/bbmap:38.90--he522d1c_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 4326149c796..82ecb35cdad 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,7 +2,7 @@ process BBMAP_BBSPLIT { label 'process_high' conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) - def container_image = "/bbmap:38.93--he522d1c_0" + def container_image = "/bbmap:38.93--he522d1c_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index 6e4938af95f..8563a1f8cf9 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -4,7 +4,7 @@ process BBMAP_CLUMPIFY { label 'process_high_memory' conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) - def container_image = "/bbmap:38.98--h5c4e2a8_1" + def container_image = "/bbmap:38.98--h5c4e2a8_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index c965e523d48..1fdf2a7e3a0 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -3,7 +3,7 @@ process BBMAP_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) - def container_image = "/bbmap:38.92--he522d1c_0" + def container_image = "/bbmap:38.92--he522d1c_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index a4f0e718a32..de6bfede58b 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -3,7 +3,7 @@ process BBMAP_PILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" + def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index f9c7d57be26..7a501948c4b 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_ANNOTATE { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index c1da104cdb2..5526bc95107 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_CONCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index f14348608e8..4da9c561106 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index 253ff4a8810..35eb9b3472d 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_CONVERT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 794fb4e707c..e83316082e5 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 6beb2488b19..5ff7c80a1ee 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 1b73fe3c565..9b7ce499ee1 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_ISEC { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 8e82b28b4be..27429cac3e3 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index 8439ab6fd9d..816dc7faa30 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_MPILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index bc0d8d2db21..87853ecabf0 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_NORM { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 2035b788d46..70c89d7377f 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 30b3579890e..da4b1472434 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_REHEADER { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 261717f8205..41b9711f635 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_ROH { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index ddabb0e3c9e..436d1c194c2 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index b5dc76c53a7..0792b6ac95e 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 592345fa1cf..7602dac552e 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -3,7 +3,7 @@ process BCFTOOLS_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" + def container_image = "/bcftools:1.15.1--h0ea216a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index 8316e848755..9df47150549 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_BAMTOBED { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index 6acbba401d5..c3b2e5bd307 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_COMPLEMENT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 2d3ebabe975..aa7643c189b 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index b0a8b5518b0..848fa5373c2 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_GETFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index e38e0536a63..cc0a4eb8d29 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_INTERSECT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index c4ec1bf2921..f74e8e8a906 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_MAKEWINDOWS { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--h7d7f7ad_1" + def container_image = "/bedtools:2.30.0--h7d7f7ad_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index be7a1eaf9ce..51b1caa7f23 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_MASKFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 77783be2894..b50b5a30c4c 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index 6ba688688c9..51ec0f2f685 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_SLOP { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index ac927f57e9b..17dc46cc08e 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_SORT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index 458f60782d7..23ea1eade81 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_SPLIT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--h468198e_3" + def container_image = "/bedtools:2.30.0--h468198e_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index 3f52e863a54..dcc86ed01bd 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -3,7 +3,7 @@ process BEDTOOLS_SUBTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" + def container_image = "/bedtools:2.30.0--hc088bd4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index fb47d41939c..cc3f60782db 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -3,7 +3,7 @@ process BIOBAMBAM_BAMMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - def container_image = "/biobambam:2.0.183--h9f5acd7_1" + def container_image = "/biobambam:2.0.183--h9f5acd7_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index f6bfb3a6515..3a012037a57 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -3,7 +3,7 @@ process BISCUIT_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 2687ae908f0..757064ecd2e 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -3,7 +3,7 @@ process BISCUIT_BLASTER { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index bfef7866437..6903d42f0f9 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -3,7 +3,7 @@ process BISCUIT_BSCONV { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" + def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index 9e43bb53ea4..c21e1d347ed 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -3,7 +3,7 @@ process BISCUIT_EPIREAD { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 415466a7f7c..7d982439859 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -3,7 +3,7 @@ process BISCUIT_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" + def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index c9f565063fc..7d5935dfe26 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -3,7 +3,7 @@ process BISCUIT_MERGECG { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 44c4ca84adb..b683ed7d414 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -3,7 +3,7 @@ process BISCUIT_PILEUP { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index b877e52cbc6..220cb8ae934 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -3,7 +3,7 @@ process BISCUIT_QC { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" + def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 0d1dda1320a..3bae4d43a09 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -3,8 +3,9 @@ process BISCUIT_VCF2BED { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index 0f5cdc73feb..54401f610db 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -3,7 +3,7 @@ process BISMARK_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" + def container_image = "/bismark:0.23.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index 0271ce4bc4c..b5b211276aa 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -3,7 +3,7 @@ process BISMARK_DEDUPLICATE { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" + def container_image = "/bismark:0.23.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index f851f585f70..56e7a1bbc0c 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -3,7 +3,7 @@ process BISMARK_GENOMEPREPARATION { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" + def container_image = "/bismark:0.23.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 92421fba202..a265c913a2d 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -3,7 +3,7 @@ process BISMARK_METHYLATIONEXTRACTOR { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" + def container_image = "/bismark:0.23.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 84c1f456bfd..5933747a724 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -3,7 +3,7 @@ process BISMARK_REPORT { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" + def container_image = "/bismark:0.23.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 3b64d4f9b2b..52e4fb4e502 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -2,7 +2,7 @@ process BISMARK_SUMMARY { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" + def container_image = "/bismark:0.23.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index 0c085221505..c4646bf8bec 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -3,7 +3,7 @@ process BLAST_BLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - def container_image = "/blast:2.12.0--pl5262h3289130_0" + def container_image = "/blast:2.12.0--pl5262h3289130_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index e2231c701cf..208fe8c3f86 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -3,7 +3,7 @@ process BLAST_MAKEBLASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - def container_image = "/blast:2.12.0--pl5262h3289130_0" + def container_image = "/blast:2.12.0--pl5262h3289130_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index b9dad008462..9e2f5c49b9d 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -3,7 +3,7 @@ process BLAST_TBLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - def container_image = "/blast:2.12.0--pl5262h3289130_0" + def container_image = "/blast:2.12.0--pl5262h3289130_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index af0ccc20463..513b8f0eff6 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,7 +3,7 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - def container_image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" +def container_image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) input: diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 88e6cbdbf37..4eb3ea8ecbf 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -3,7 +3,7 @@ process BOWTIE_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) - def container_image = "/bowtie:1.3.0--py38hed8969a_1" + def container_image = "/bowtie:1.3.0--py38hed8969a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index d22257ef740..2a3b2dbf39e 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -3,7 +3,7 @@ process BOWTIE2_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) - def container_image = "/bowtie2:2.4.4--py39hbb4e92a_0" + def container_image = "/bowtie2:2.4.4--py39hbb4e92a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index 167007f91c8..5912d7d8c96 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -5,7 +5,7 @@ process BRACKEN_BRACKEN { // WARN: Version information not provided by tool on CLI. // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - def container_image = "/bracken:2.7--py39hc16433a_0" + def container_image = "/bracken:2.7--py39hc16433a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 637203e98f1..86855e645db 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,7 +2,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { label 'process_low' conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - def container_image = "/bracken:2.7--py39hc16433a_0" + def container_image = "/bracken:2.7--py39hc16433a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index d6660e65f20..162b8199d5d 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -3,8 +3,9 @@ process BUSCO { label 'process_medium' conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) - def container_image = "/busco:5.4.3--pyhdfd78af_0" + def container_image = "/busco:5.4.3--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index e5a40c89a5f..f3fd23895b0 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -3,7 +3,7 @@ process BWA_ALN { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - def container_image = "/bwa:0.7.17--h5bf99c6_8" + def container_image = "/bwa:0.7.17--h5bf99c6_8" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index b4e6bfe93d0..fc1c08302fd 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -3,8 +3,9 @@ process BWA_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - def container_image = "/bwa:0.7.17--hed695b0_7" + def container_image = "/bwa:0.7.17--hed695b0_7" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index d8f8e3e9c05..15e138ca15e 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -3,8 +3,9 @@ process BWA_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 8e6b5bd1cbe..3480cba9cdf 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -3,8 +3,9 @@ process BWA_SAMPE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index b36d4e617c9..224a686b0c0 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -3,7 +3,7 @@ process BWA_SAMSE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index b3d4c444e85..d61c1ef6bf8 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -3,8 +3,9 @@ process BWAMEM2_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) - def container_image = "/bwa-mem2:2.2.1--he513fc3_0" + def container_image = "/bwa-mem2:2.2.1--he513fc3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index ba9daf05533..93f13141ca8 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -3,8 +3,9 @@ process BWAMEM2_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" + def container_image = "/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 911f9f388e2..0cc44590b01 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -3,7 +3,7 @@ process BWAMETH_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - def container_image = "/bwameth:0.2.2--py_1" + def container_image = "/bwameth:0.2.2--py_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index dcc798831b3..954b7f06da5 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -3,7 +3,7 @@ process BWAMETH_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - def container_image = "/bwameth:0.2.2--py_1" + def container_image = "/bwameth:0.2.2--py_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index c4f642ece43..13abc0293c7 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -3,7 +3,7 @@ process CAT_CAT { label 'process_low' conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) - def container_image = "/pigz:2.3.4" + def container_image = "/pigz:2.3.4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index fd69ee5c02c..2ea69fef0cd 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,7 +3,7 @@ process CAT_FASTQ { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - def container_image = "/ubuntu:20.04" + def container_image = "/ubuntu:20.04" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 61725726939..467dc07bfc0 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -3,7 +3,7 @@ process CENTRIFUGE_CENTRIFUGE { label 'process_high' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" + def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 6669e9640f5..a9dc06d3f31 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -3,7 +3,7 @@ process CENTRIFUGE_KREPORT { label 'process_single' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" + def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index d02bfdb3e3f..82273e4dca0 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -3,7 +3,7 @@ process CHECKM_LINEAGEWF { label 'process_medium' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" + def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 5ce62a5e9ad..079eb5cbb7e 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -3,7 +3,7 @@ process CHECKM_QA { label 'process_low' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" + def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index 04f95c5965c..839b76806fd 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -3,7 +3,7 @@ process CHROMAP_CHROMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" + def container_image = "/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 4f3e44f05be..9ba87bca3e6 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -3,7 +3,7 @@ process CHROMAP_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) - def container_image = "/chromap:0.2.1--hd03093a_0" + def container_image = "/chromap:0.2.1--hd03093a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 31586b0981b..1209b3e7371 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -3,8 +3,9 @@ process CLONALFRAMEML { label 'process_low' conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) - def container_image = "/clonalframeml:1.12--h7d875b9_1" + def container_image = "/clonalframeml:1.12--h7d875b9_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index 392fd8bcf23..f0d92780e2a 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -4,7 +4,7 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) - def container_image = "/cmseq:1.0.4--pyhb7b1952_0" + def container_image = "/cmseq:1.0.4--pyhb7b1952_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index ad2f9347794..b5f95e70cf0 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -3,7 +3,7 @@ process CNVKIT_ANTITARGET { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" + def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index a1f1ce11d8c..43e05371f1e 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -3,7 +3,7 @@ process CNVKIT_BATCH { label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) - def container_image = "/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" + def container_image = "/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 737918d861f..34020c34615 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -3,7 +3,7 @@ process CNVKIT_REFERENCE { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" + def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index 705a7d9be54..73a8f884c2b 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -3,7 +3,7 @@ process CNVPYTOR_CALLCNVS { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 93eea866318..3b5fbc68dac 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -3,7 +3,7 @@ process CNVPYTOR_HISTOGRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index 3a15bdaf584..1164c322918 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -3,7 +3,7 @@ process CNVPYTOR_IMPORTREADDEPTH { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index a2b05f424c2..fbcbab4acf3 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -3,7 +3,7 @@ process CNVPYTOR_PARTITION { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index 1cd1bfbf886..c3e08baed17 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -3,7 +3,7 @@ process CNVPYTOR_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" + def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 20b376df9fe..dae09d80d61 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -3,7 +3,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" + def container_image = "/control-freec:11.6--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 6093d6c40d7..133db341df9 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -3,7 +3,7 @@ process CONTROLFREEC_FREEC { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" + def container_image = "/control-freec:11.6--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index 6b67c7ee559..e2c6814b4fa 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -3,7 +3,7 @@ process CONTROLFREEC_FREEC2BED { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" + def container_image = "/control-freec:11.6--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 93e9dd97e99..959cdcb8d1e 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -3,7 +3,7 @@ process CONTROLFREEC_FREEC2CIRCOS { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" + def container_image = "/control-freec:11.6--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index f47817371f6..ccd9610a5ef 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -3,7 +3,7 @@ process CONTROLFREEC_MAKEGRAPH { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" + def container_image = "/control-freec:11.6--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 5dd75e6e9a0..d8a424104ce 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -3,7 +3,7 @@ process COOLER_CLOAD { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" + def container_image = "/cooler:0.8.11--pyh3252c3a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index bfc5aa1c069..7b46ca4c5c2 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -3,7 +3,7 @@ process COOLER_DIGEST { label 'process_medium' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" + def container_image = "/cooler:0.8.11--pyh3252c3a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index edc075dbc44..2ca1788320d 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -3,7 +3,7 @@ process COOLER_DUMP { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" + def container_image = "/cooler:0.8.11--pyh3252c3a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index b266d9940d0..64daf1fb189 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -3,7 +3,7 @@ process COOLER_MERGE { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" + def container_image = "/cooler:0.8.11--pyh3252c3a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 16ed78a56b3..ac96ec348ff 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -3,7 +3,7 @@ process COOLER_ZOOMIFY { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" + def container_image = "/cooler:0.8.11--pyh3252c3a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index ad85e1ba879..762b23ab0c7 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -3,7 +3,7 @@ process CRUMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) - def container_image = "/crumble:0.9.0--hb0d9459_1" + def container_image = "/crumble:0.9.0--hb0d9459_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 27f9baa4a9e..e5b0a7d2853 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -3,7 +3,7 @@ process CSVTK_CONCAT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - def container_image = "/csvtk:0.23.0--h9ee0642_0" + def container_image = "/csvtk:0.23.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 7e66f8ab4c1..2004106b7f5 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -3,7 +3,7 @@ process CSVTK_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - def container_image = "/csvtk:0.23.0--h9ee0642_0" + def container_image = "/csvtk:0.23.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c837de10e70..6d82d817d0b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -3,7 +3,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - def container_image = "/multiqc:1.13--pyhdfd78af_0" + def container_image = "/multiqc:1.13--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index d22d04e6079..a57f9ad5016 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -3,7 +3,7 @@ process CUSTOM_GETCHROMSIZES { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 3a2d7041580..74392792ffe 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -3,7 +3,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" + def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 4f013d2a860..274a6971311 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -3,7 +3,7 @@ process CUTADAPT { label 'process_medium' conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) - def container_image = "/cutadapt:3.4--py39h38f01e4_1" + def container_image = "/cutadapt:3.4--py39h38f01e4_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index 6573585856c..dfbea26270c 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -3,7 +3,7 @@ process DAMAGEPROFILER { label 'process_single' conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) - def container_image = "/damageprofiler:1.1--hdfd78af_2" + def container_image = "/damageprofiler:1.1--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index 9e9d41614ec..693caca5e10 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -3,8 +3,9 @@ process DASTOOL_DASTOOL { label 'process_medium' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - def container_image = "/das_tool:1.1.4--r41hdfd78af_1" + def container_image = "/das_tool:1.1.4--r41hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index 5cfa666f704..add35400739 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -3,8 +3,9 @@ process DASTOOL_FASTATOCONTIG2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - def container_image = "/das_tool:1.1.4--r41hdfd78af_1" + def container_image = "/das_tool:1.1.4--r41hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 9972bc56c5a..0b3cd5735e2 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -3,8 +3,9 @@ process DASTOOL_SCAFFOLDS2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) - def container_image = "/das_tool:1.1.3--r41hdfd78af_0" + def container_image = "/das_tool:1.1.3--r41hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index 3f34dba9178..cd3f006fef6 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -3,8 +3,8 @@ process DEDUP { label 'process_single' conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) - def container_image = "/dedup:0.12.8--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "/dedup:0.12.8--hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index f7aaf9e8b63..46b2d9262f5 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,7 +2,7 @@ process DEEPARG_DOWNLOADDATA { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - def container_image = "/deeparg:1.0.2--pyhdfd78af_1" + def container_image = "/deeparg:1.0.2--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 2bb07b8a2e1..236858986ce 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -3,7 +3,7 @@ process DEEPARG_PREDICT { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - def container_image = "/deeparg:1.0.2--pyhdfd78af_1" + def container_image = "/deeparg:1.0.2--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index be5f69f6ac7..99491ff255b 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -2,7 +2,7 @@ process DEEPBGC_DOWNLOAD { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" + def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index 1986cb0820e..d28d630a4ad 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -3,7 +3,7 @@ process DEEPBGC_PIPELINE { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" + def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index f19eab725e8..974b2c16529 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_BAMCOVERAGE { label 'process_low' conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" + def container_image = "/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 6b733606618..c2a259a17f0 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_COMPUTEMATRIX { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" + def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index d5396ba699f..ee7a7bd4078 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_PLOTFINGERPRINT { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" + def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index a997abb7b9f..ebd435c2350 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_PLOTHEATMAP { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" + def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index b8fc60c43dd..c2054fb870a 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_PLOTPROFILE { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" + def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index b2a1c9d09a3..6069c353482 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -3,7 +3,7 @@ process DELLY_CALL { label 'process_medium' conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) - def container_image = "/delly:1.1.5--h358d541_0" + def container_image = "/delly:1.1.5--h358d541_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index 68d3cb82f12..33c2bf0612e 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -3,7 +3,7 @@ process DIAMOND_BLASTP { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - def container_image = "/diamond:2.0.15--hb97b32f_0" + def container_image = "/diamond:2.0.15--hb97b32f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 6b170d05506..e25fb93a31c 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -3,7 +3,7 @@ process DIAMOND_BLASTX { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - def container_image = "/diamond:2.0.15--hb97b32f_0" + def container_image = "/diamond:2.0.15--hb97b32f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index 52994d4f82d..f7f3d1bd5e8 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -3,7 +3,7 @@ process DIAMOND_MAKEDB { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - def container_image = "/diamond:2.0.15--hb97b32f_0" + def container_image = "/diamond:2.0.15--hb97b32f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index ebd2967aa1b..d80599b0cd7 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -3,7 +3,7 @@ process DRAGMAP_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) - def container_image = "/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" + def container_image = "/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index b665dee6817..737c5c9237b 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -3,7 +3,7 @@ process DRAGMAP_HASHTABLE { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) - def container_image = "/dragmap:1.2.1--hd4ca14e_0" + def container_image = "/dragmap:1.2.1--hd4ca14e_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index de209c7bea4..860c932af7c 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -3,8 +3,9 @@ process DRAGONFLYE { label 'process_medium' conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) - def container_image = "/dragonflye:1.0.11--hdfd78af_0" + def container_image = "/dragonflye:1.0.11--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 24ed2cab53f..f4869027b00 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -3,8 +3,9 @@ process DSHBIO_EXPORTSEGMENTS { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" + def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index e1723f5a864..674372c84ac 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -3,8 +3,9 @@ process DSHBIO_FILTERBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" + def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index 054b715e75e..4990698ec1a 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -3,8 +3,9 @@ process DSHBIO_FILTERGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" + def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index ace2aadbd42..e7e27ff7b33 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -3,8 +3,9 @@ process DSHBIO_SPLITBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" + def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 7be6819fc7b..4fc93947e46 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -3,8 +3,9 @@ process DSHBIO_SPLITGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" + def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 655b9777a6f..ba4a38c3d74 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -3,7 +3,7 @@ process ECTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) - def container_image = "/ectyper:1.0.0--pyhdfd78af_1" + def container_image = "/ectyper:1.0.0--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index c4b76804921..0604c9b131b 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -3,8 +3,9 @@ process ELPREP_FILTER { label 'process_high' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - def container_image = "/elprep:5.1.2--he881be0_0" + def container_image = "/elprep:5.1.2--he881be0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index 0175dddc605..c403ac880c7 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -3,7 +3,7 @@ process ELPREP_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - def container_image = "/elprep:5.1.2--he881be0_0" + def container_image = "/elprep:5.1.2--he881be0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 2cd76a3fd3c..8ba666759e3 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -3,7 +3,7 @@ process ELPREP_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - def container_image = "/elprep:5.1.2--he881be0_0" + def container_image = "/elprep:5.1.2--he881be0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 5d456f25de2..3a752c96580 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -3,7 +3,7 @@ process EMBOSS_SEQRET { label 'process_single' conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) - def container_image = "/emboss:6.6.0--hf657eab_5" + def container_image = "/emboss:6.6.0--hf657eab_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index e31a6e3a60c..5974c362580 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -3,7 +3,7 @@ process EMMTYPER { label 'process_low' conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) - def container_image = "/emmtyper:0.2.0--py_0" + def container_image = "/emmtyper:0.2.0--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 87cf4968cf9..245305faad6 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -3,8 +3,9 @@ process ENDORSPY { label 'process_low' conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) - def container_image = "/endorspy:0.4--hdfd78af_0" + def container_image = "/endorspy:0.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index e46599352ad..47737aa9688 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -3,7 +3,7 @@ process ENSEMBLVEP { label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) - def container_image = "/ensembl-vep:106.1--pl5321h4a94de4_0" + def container_image = "/ensembl-vep:106.1--pl5321h4a94de4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 8506407bc5a..77574bdd286 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -3,7 +3,7 @@ process ENTREZDIRECT_ESEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - def container_image = "/entrez-direct:16.2--he881be0_1" + def container_image = "/entrez-direct:16.2--he881be0_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index ee933331997..25f79c0e0fe 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -3,7 +3,7 @@ process ENTREZDIRECT_ESUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - def container_image = "/entrez-direct:16.2--he881be0_1" + def container_image = "/entrez-direct:16.2--he881be0_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index 588926a6412..144de51f913 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -3,7 +3,7 @@ process ENTREZDIRECT_XTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - def container_image = "/entrez-direct:16.2--he881be0_1" +def container_image = "/entrez-direct:16.2--he881be0_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index 77495e9e490..165ed3f2b4c 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -3,7 +3,7 @@ process EPANG { label 'process_high' conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) - def container_image = "/epa-ng:0.3.8--h9a82719_1" + def container_image = "/epa-ng:0.3.8--h9a82719_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index c165b2934bf..ba517b556ce 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -3,7 +3,7 @@ process EXPANSIONHUNTER { label 'process_low' conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) - def container_image = "/expansionhunter:4.0.2--he785bd8_0" + def container_image = "/expansionhunter:4.0.2--he785bd8_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index 8d21e30489e..ae51019e658 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -3,7 +3,7 @@ process FAQCS { label 'process_medium' conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) - def container_image = "/faqcs%3A2.10--r41h9a82719_2" + def container_image = "/faqcs%3A2.10--r41h9a82719_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index f830e6306cc..b3bbb6987e5 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -4,7 +4,7 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) - def container_image = "/fargene:0.1--py27h21c881e_4" + def container_image = "/fargene:0.1--py27h21c881e_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index 6a0cb361bc4..5928d85cea1 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -3,7 +3,7 @@ process FASTANI { label 'process_medium' conda (params.enable_conda ? "bioconda::fastani=1.32" : null) - def container_image = "/fastani:1.32--he1c1bb9_0" + def container_image = "/fastani:1.32--he1c1bb9_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index 853c76c4f16..6e84dd4c1c8 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -3,8 +3,9 @@ process FASTAWINDOWS { label 'process_low' conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) - def container_image = "/fasta_windows:0.2.4--hec16e2b_0" + def container_image = "/fasta_windows:0.2.4--hec16e2b_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 0305d1b938a..823fb5fa547 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -3,8 +3,9 @@ process FASTP { label 'process_medium' conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) - def container_image = "/fastp:0.23.2--h79da9fb_0" + def container_image = "/fastp:0.23.2--h79da9fb_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index bfa74600fc5..698e0aa48ce 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -3,7 +3,7 @@ process FASTQC { label 'process_medium' conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - def container_image = "/fastqc:0.11.9--0" + def container_image = "/fastqc:0.11.9--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index ac1ccd1a409..a6945e7c8f4 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -3,7 +3,7 @@ process FASTQSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) - def container_image = "/fastq-scan:0.4.4--h7d875b9_0" + def container_image = "/fastq-scan:0.4.4--h7d875b9_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 01760e3f274..695bd1e1fed 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -2,8 +2,9 @@ process FASTTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) - def container_image = "/fasttree:2.1.10--h516909a_4" + def container_image = "/fasttree:2.1.10--h516909a_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path alignment diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 118f087dc84..7979417787a 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -3,8 +3,9 @@ process FFQ { label 'process_low' conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) - def container_image = "/ffq:0.2.1--pyhdfd78af_0" + def container_image = "/ffq:0.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 92b60f320a9..65f00822fe1 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -3,7 +3,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" + def container_image = "/fgbio:2.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index eede7f7a899..df90958ce3c 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -3,7 +3,7 @@ process FGBIO_FASTQTOBAM { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" + def container_image = "/fgbio:2.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 4b57de9ffed..06b3194e747 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -3,7 +3,7 @@ process FGBIO_GROUPREADSBYUMI { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" + def container_image = "/fgbio:2.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index 4516f3f9f83..bd3c4bb535a 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -3,7 +3,7 @@ process FGBIO_SORTBAM { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" + def container_image = "/fgbio:2.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 35195aff6cf..434c8a3c36b 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -3,7 +3,7 @@ process FGBIO_ZIPPERBAMS { label 'process_single' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" + def container_image = "/fgbio:2.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index f0e1e060a7f..a331ded8cc0 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -3,7 +3,7 @@ process FILTLONG { label 'process_low' conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) - def container_image = "/filtlong:0.2.1--h9a82719_0" + def container_image = "/filtlong:0.2.1--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index 30f26057056..c2b5ac9b82e 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -2,7 +2,7 @@ process FLASH { tag "$meta.id" label 'process_medium' - def container_image = "/flash:1.2.11--hed695b0_5" + def container_image = "/flash:1.2.11--hed695b0_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 68ca1e737c3..2ad053cd465 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -3,8 +3,9 @@ process FLYE { label 'process_high' conda (params.enable_conda ? "bioconda::flye=2.9" : null) - def container_image = "/flye:2.9--py39h6935b12_1" + def container_image = "/flye:2.9--py39h6935b12_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 86915263945..db9e79a18b5 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -3,7 +3,7 @@ process FREEBAYES { label 'process_low' conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) - def container_image = "/freebayes:1.3.5--py38ha193a2f_3" + def container_image = "/freebayes:1.3.5--py38ha193a2f_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index b53de55b41b..e184b2bd9de 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -5,7 +5,7 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) - def container_image = "/gamma%3A2.1--hdfd78af_0" + def container_image = "/gamma%3A2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index fb635ca9a68..1bd28feb658 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -3,8 +3,9 @@ process GAPPA_EXAMINEASSIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - def container_image = "/gappa:0.8.0--h9a82719_0" + def container_image = "/gappa:0.8.0--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 7489e67447b..013854da8f4 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -3,8 +3,9 @@ process GAPPA_EXAMINEGRAFT { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - def container_image = "/gappa:0.8.0--h9a82719_0" + def container_image = "/gappa:0.8.0--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 19be805b1d7..47540550260 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -3,8 +3,9 @@ process GAPPA_EXAMINEHEATTREE { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - def container_image = "/gappa:0.8.0--h9a82719_0" + def container_image = "/gappa:0.8.0--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 0b3aedacce1..721a81beb3c 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -3,7 +3,7 @@ process GATK_INDELREALIGNER { label 'process_single' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - def container_image = "/gatk:3.5--hdfd78af_11" + def container_image = "/gatk:3.5--hdfd78af_11" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index eae92b37788..93673eee6f2 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -3,7 +3,7 @@ process GATK_REALIGNERTARGETCREATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - def container_image = "/gatk:3.5--hdfd78af_11" + def container_image = "/gatk:3.5--hdfd78af_11" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 8709e15f8e6..d314ae4bf34 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -3,7 +3,7 @@ process GATK_UNIFIEDGENOTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - def container_image = "/gatk:3.5--hdfd78af_11" + def container_image = "/gatk:3.5--hdfd78af_11" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 00e3c1b32fe..5c98a3bf652 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -3,7 +3,7 @@ process GATK4_APPLYBQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 966bc6b8bc3..82c197e16c2 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -3,7 +3,7 @@ process GATK4_APPLYVQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index fc1b3ef14b3..20c669fc144 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -3,7 +3,7 @@ process GATK4_BASERECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index a80400dc53f..8b21e323a78 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -3,7 +3,7 @@ process GATK4_BEDTOINTERVALLIST { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index d106cdf682d..f20566296e1 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -3,7 +3,7 @@ process GATK4_CALCULATECONTAMINATION { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 3a2a5f81af1..6035de8121e 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -3,8 +3,9 @@ process GATK4_CALIBRATEDRAGSTRMODEL { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index a77a18804be..96d2e167b01 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -3,7 +3,7 @@ process GATK4_COLLECTREADCOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index bd8556a7cf8..2e67748b856 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -3,7 +3,7 @@ process GATK4_COLLECTSVEVIDENCE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 2dc9563b8eb..370c6b256f9 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -3,7 +3,7 @@ process GATK4_COMBINEGVCFS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 574aa1c99ab..6a6f7851972 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -3,7 +3,7 @@ process GATK4_COMPOSESTRTABLEFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 4455f99dd1d..ab99054765f 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -3,7 +3,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 32cffc7b2d0..e3b3738c29a 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -3,7 +3,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 758feceb294..39ae064093f 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -3,7 +3,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 38d11641871..8cc3c638c58 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -3,7 +3,7 @@ process GATK4_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index bbfed0f908b..31ef85c4d06 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -3,7 +3,7 @@ process GATK4_FILTERVARIANTTRANCHES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index ea8975576d3..c271e5e191d 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -3,8 +3,9 @@ process GATK4_GATHERBQSRREPORTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index e6339d44c19..b4a69bd5b11 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -3,7 +3,7 @@ process GATK4_GATHERPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 86c09bcbb0e..4a840ed5b9f 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -3,7 +3,7 @@ process GATK4_GENOMICSDBIMPORT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 0ce81fb2001..863858417fd 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -3,8 +3,9 @@ process GATK4_GENOTYPEGVCFS { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index ec5e06d8d85..9a11fb4ee9c 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -3,7 +3,7 @@ process GATK4_GETPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 9081413b7a9..83fe3296c26 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -3,7 +3,7 @@ process GATK4_HAPLOTYPECALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 1ec648510d6..32924ff2cef 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -3,7 +3,7 @@ process GATK4_INDEXFEATUREFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index a37c069faf2..3354ce12618 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -3,7 +3,7 @@ process GATK4_INTERVALLISTTOBED { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 79b6715e9f6..8fb194ec1e6 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -3,7 +3,7 @@ process GATK4_INTERVALLISTTOOLS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index c5e3e67faa3..9daf8cbf429 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -3,7 +3,7 @@ process GATK4_LEARNREADORIENTATIONMODEL { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index c47f9fc7bba..cde0ec474e0 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -3,7 +3,7 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 578b26d786c..334b971e5e5 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -3,7 +3,7 @@ process GATK4_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index c1768fe695f..8d1986b7aa6 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -3,7 +3,7 @@ process GATK4_MERGEBAMALIGNMENT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 075d08bb8b9..758a0c41439 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -3,7 +3,7 @@ process GATK4_MERGEMUTECTSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 176e15833c2..a0b67fcba63 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -3,7 +3,7 @@ process GATK4_MERGEVCFS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 0e850eb4dad..7ba9cedcf69 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -3,7 +3,7 @@ process GATK4_MUTECT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 0182239e5f8..d744988dbff 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -3,7 +3,7 @@ process GATK4_PRINTSVEVIDENCE { label 'process_single' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index a66b578ed9b..75ec7370a73 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -3,7 +3,7 @@ process GATK4_REBLOCKGVCF { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 00d8100f647..7a61d91b5ce 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -3,7 +3,7 @@ process GATK4_REVERTSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 353bab8d6e0..89111d57f3e 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -3,7 +3,7 @@ process GATK4_SAMTOFASTQ { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 2a2c1cb94ce..018e633b387 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -3,8 +3,9 @@ process GATK4_SELECTVARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index 1421a6f4171..b50b8fa18ab 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -3,7 +3,7 @@ process GATK4_SPLITINTERVALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 19d1b4902a8..8ace4b68e56 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -3,7 +3,7 @@ process GATK4_SPLITNCIGARREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index cc3a8d9f79f..cbafd73df92 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -3,7 +3,7 @@ process GATK4_VARIANTFILTRATION { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 37659a88062..a679c2f39dc 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -3,7 +3,7 @@ process GATK4_VARIANTRECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index 9ae078fa093..2a5cf5d071e 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -3,7 +3,7 @@ process GECCO_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) - def container_image = "/gecco:0.9.2--pyhdfd78af_0" + def container_image = "/gecco:0.9.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 9bec567251f..08f78f298bd 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -3,7 +3,7 @@ process GENMAP_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - def container_image = "/genmap:1.3.0--h1b792b2_1" + def container_image = "/genmap:1.3.0--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index c1b5e099307..a2249f1cdce 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -3,7 +3,7 @@ process GENMAP_MAPPABILITY { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - def container_image = "/genmap:1.3.0--h1b792b2_1" + def container_image = "/genmap:1.3.0--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index e65e44b2343..bb9f0934d55 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -3,8 +3,9 @@ process GENMOD_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 9ec37befba1..ae8647a633d 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -3,8 +3,9 @@ process GENMOD_COMPOUND { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index e4b49ae084c..97e05b226a1 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -3,8 +3,9 @@ process GENMOD_MODELS { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index d1d843d3717..dca44cda3af 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -3,8 +3,9 @@ process GENMOD_SCORE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" + def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index 2773643c78f..6b435ba39bf 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -3,7 +3,7 @@ process GENOMESCOPE2 { label 'process_low' conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) - def container_image = "/genomescope2:2.0--py310r41hdfd78af_5" + def container_image = "/genomescope2:2.0--py310r41hdfd78af_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index 8263cb2bbee..60d943fc213 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -3,8 +3,9 @@ process GENOTYPHI_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) - def container_image = "/genotyphi:1.9.1--hdfd78af_1" + def container_image = "/genotyphi:1.9.1--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 863b0b1b4f6..1346ea5508c 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -3,7 +3,7 @@ process GENRICH { label 'process_high' conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) - def container_image = "/genrich:0.6.1--h5bf99c6_1" + def container_image = "/genrich:0.6.1--h5bf99c6_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index ea4b0e69b2f..d3c66e4d606 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -4,7 +4,7 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) - def container_image = "/gfaffix:0.1.4--hec16e2b_0" + def container_image = "/gfaffix:0.1.4--hec16e2b_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 5ec23c1ea59..db8cf75a7cf 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -3,8 +3,9 @@ process GFFREAD { label 'process_low' conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) - def container_image = "/gffread:0.12.1--h8b12597_0" + def container_image = "/gffread:0.12.1--h8b12597_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index dcc25bb85c6..6f18132bcf3 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -3,7 +3,7 @@ process GLIMPSE_CHUNK { label 'process_medium' conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) - def container_image = "/glimpse-bio:1.1.1--h2ce4488_2" + def container_image = "/glimpse-bio:1.1.1--h2ce4488_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 1f07001b8bb..c92fdedebc1 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -3,7 +3,7 @@ process GLNEXUS { label 'process_medium' conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) - def container_image = "/glnexus:1.4.1--h40d77a6_0" + def container_image = "/glnexus:1.4.1--h40d77a6_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index f23b379599d..6e0314cd4be 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -3,7 +3,7 @@ process GOAT_TAXONSEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) - def container_image = "/goat:0.2.0--h92d785c_0" + def container_image = "/goat:0.2.0--h92d785c_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index db2ee1831ca..cf89fafe0e4 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -4,7 +4,7 @@ process GRAPHMAP2_ALIGN { tag "$meta.id" conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - def container_image = "/graphmap:0.6.3--he513fc3_0" + def container_image = "/graphmap:0.6.3--he513fc3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index 7ed53ed9118..79cd43f4e7d 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -2,7 +2,7 @@ process GRAPHMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - def container_image = "/graphmap:0.6.3--he513fc3_0" + def container_image = "/graphmap:0.6.3--he513fc3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index 61f3016bc74..a57f78ec13b 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -3,7 +3,7 @@ process GSTAMA_COLLAPSE { label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - def container_image = "/gs-tama:1.0.3--hdfd78af_0" + def container_image = "/gs-tama:1.0.3--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 42342b6ceb6..d34211e9839 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -3,7 +3,7 @@ process GSTAMA_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) - def container_image = "/gs-tama:1.0.2--hdfd78af_0" + def container_image = "/gs-tama:1.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index 666fb5e673d..b01e0c26bd3 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -3,7 +3,7 @@ process GSTAMA_POLYACLEANUP { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - def container_image = "/gs-tama:1.0.3--hdfd78af_0" + def container_image = "/gs-tama:1.0.3--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index a0eaba9772b..403206977c9 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -4,7 +4,7 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) - def container_image = "/gtdbtk:1.5.0--pyhdfd78af_0" + def container_image = "/gtdbtk:1.5.0--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 380195c635f..278f12d723f 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -2,8 +2,9 @@ process GUBBINS { label 'process_medium' conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) - def container_image = "/gubbins:3.0.0--py39h5bf99c6_0" + def container_image = "/gubbins:3.0.0--py39h5bf99c6_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index ecbe459754d..552cca2be7e 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -3,7 +3,7 @@ process GUNC_DOWNLOADDB { label 'process_single' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - def container_image = "/gunc:1.0.5--pyhdfd78af_0" + def container_image = "/gunc:1.0.5--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index b7890ae56a1..1578021e5d6 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -3,7 +3,7 @@ process GUNC_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - def container_image = "/gunc:1.0.5--pyhdfd78af_0" + def container_image = "/gunc:1.0.5--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 43707a3288a..33929b1ab1d 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -3,7 +3,7 @@ process GUNZIP { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - def container_image = "/ubuntu:20.04" + def container_image = "/ubuntu:20.04" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index 5b2c5ff123a..368d47126a0 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -3,7 +3,7 @@ process GVCFTOOLS_EXTRACTVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) - def container_image = "/gvcftools:0.17.0--he941832_3" + def container_image = "/gvcftools:0.17.0--he941832_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 5593f922bf8..d80d71f2d24 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -3,7 +3,7 @@ process HAMRONIZATION_ABRICATE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index 127914c43b3..0d29d46a368 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -3,7 +3,7 @@ process HAMRONIZATION_AMRFINDERPLUS { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index ddc729a2ac2..cd78db54f6f 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -3,7 +3,7 @@ process HAMRONIZATION_DEEPARG { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index cd687f52843..639b09e844a 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -3,7 +3,7 @@ process HAMRONIZATION_FARGENE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index 99427bd39ed..e0687d4140f 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -3,7 +3,7 @@ process HAMRONIZATION_RGI { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index dddb66b9491..0c4d78b1897 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -2,7 +2,7 @@ process HAMRONIZATION_SUMMARIZE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" + def container_image = "/hamronization:1.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index fe711f44e95..ca023330571 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -3,7 +3,7 @@ process HAPLOCHECK { label 'process_low' conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) - def container_image = "/haplocheck:1.3.3--h4a94de4_0" + def container_image = "/haplocheck:1.3.3--h4a94de4_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 0dbbcb06ea3..0e5e1b72bca 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -3,8 +3,9 @@ process HAPLOGREP2_CLASSIFY { label 'process_low' conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) - def container_image = "/haplogrep:2.4.0--hdfd78af_0" + def container_image = "/haplogrep:2.4.0--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index 3e400e6d574..b67e35cc1e6 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -4,8 +4,9 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" + def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index a4b82bab5b3..4ab843eb197 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -4,7 +4,7 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" + def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index f13df93c87d..6410050c263 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -3,7 +3,7 @@ process HICAP { label 'process_low' conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) - def container_image = "/hicap:1.0.3--py_0" + def container_image = "/hicap:1.0.3--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index 7d72bd88f1b..048095bc438 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -3,7 +3,7 @@ process HIFIASM { label 'process_high' conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) - def container_image = "/hifiasm:0.15.4--h2e03b76_0" + def container_image = "/hifiasm:0.15.4--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 15e8a3dd70f..790abfb14a8 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -4,8 +4,9 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" + def container_image = "/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index d58d2b736d0..25addfb210a 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -5,7 +5,7 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - def container_image = "/hisat2:2.2.1--h1b792b2_3" + def container_image = "/hisat2:2.2.1--h1b792b2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 2fb690b7846..7aa0fb4b687 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -4,7 +4,7 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - def container_image = "/hisat2:2.2.1--h1b792b2_3" + def container_image = "/hisat2:2.2.1--h1b792b2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 5e8ee115f71..9ac135559b6 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -3,7 +3,7 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 63f41c3544a..cb06b02570b 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -4,7 +4,7 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index ed23dcc6f67..8cca042e7d8 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -3,7 +3,7 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 436249fbfe8..1e39cd3c3dc 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -4,7 +4,7 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" + def container_image = "/hmmcopy:0.1.1--h2e03b76_7" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index f017436ee23..a044208d865 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -3,7 +3,7 @@ process HMMER_ESLALIMASK { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" + def container_image = "/hmmer:3.3.2--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 2d3d3bf9bc1..c333f6b2926 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -3,8 +3,9 @@ process HMMER_ESLREFORMAT { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" + def container_image = "/hmmer:3.3.2--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 8a1fdcf62ec..d93c4e2864f 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -3,7 +3,7 @@ process HMMER_HMMALIGN { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" + def container_image = "/hmmer:3.3.2--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 4b9eedd1c5c..7ec3c106b99 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -3,7 +3,7 @@ process HMMER_HMMBUILD { label 'process_low' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h87f3376_2" + def container_image = "/hmmer:3.3.2--h87f3376_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 1f66d3174db..5d1f0a30440 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -3,8 +3,9 @@ process HMMER_HMMSEARCH { label 'process_medium' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" + def container_image = "/hmmer:3.3.2--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index 0171ce80b52..4bd8ed42232 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -3,7 +3,7 @@ process HMTNOTE { label 'process_low' conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) - def container_image = "/hmtnote:0.7.2--pyhdfd78af_0" + def container_image = "/hmtnote:0.7.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index c2048517257..6780afd09fa 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -4,8 +4,9 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" + def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index f276fc22ce4..97246ff570f 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -4,8 +4,9 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" + def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 91398f53a32..77264b39861 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,8 +5,9 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) - def container_image = "/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" + def container_image = "/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 5d32793c996..18fe039056f 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -4,8 +4,9 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" + def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index a9b6e421165..d60443af644 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -4,8 +4,9 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" + def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index c1cc2242580..bbc784513c0 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -4,7 +4,7 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) - def container_image = "/hpsuissero%3A1.0.1--hdfd78af_0" + def container_image = "/hpsuissero%3A1.0.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index c093decc5a3..ec4e5f5ce56 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -3,7 +3,7 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" + def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index 7ef4a87544b..85e81f023d1 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -4,7 +4,7 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" + def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index af5b4f7028c..9ecf0f50353 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -3,7 +3,7 @@ process IDR { label 'process_low' conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) - def container_image = "/idr:2.0.4.2--py39hcbe4a3b_5" + def container_image = "/idr:2.0.4.2--py39hcbe4a3b_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index 122497e1146..d9e21ce3032 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -3,7 +3,7 @@ process INSTRAIN_PROFILE { label 'process_high' conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) - def container_image = "/instrain:1.6.1--pyhdfd78af_0" + def container_image = "/instrain:1.6.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index 473bf5bb9b3..a68b93fd8df 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -3,7 +3,7 @@ process IQTREE { label 'process_medium' conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) - def container_image = "/iqtree:2.1.4_beta--hdcc8f71_0" + def container_image = "/iqtree:2.1.4_beta--hdcc8f71_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index 7ac02d04fe1..cf65f31bd8d 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -3,7 +3,7 @@ process ISMAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) - def container_image = "/ismapper:2.0.2--pyhdfd78af_1" + def container_image = "/ismapper:2.0.2--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index a55e02eee7f..fa2616829cd 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -3,7 +3,7 @@ process ISOSEQ3_CLUSTER { label 'process_medium' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - def container_image = "/isoseq3:3.4.0--0" + def container_image = "/isoseq3:3.4.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index 033e349f5ed..c8f62a37069 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -3,7 +3,7 @@ process ISOSEQ3_REFINE { label 'process_low' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - def container_image = "/isoseq3:3.4.0--0" + def container_image = "/isoseq3:3.4.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 69b9750dc4f..58c4f14146f 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -3,7 +3,7 @@ process IVAR_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - def container_image = "/ivar:1.3.1--h089eab3_0" + def container_image = "/ivar:1.3.1--h089eab3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index a75049ffeda..117051e6a46 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -3,7 +3,7 @@ process IVAR_TRIM { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - def container_image = "/ivar:1.3.1--h089eab3_0" + def container_image = "/ivar:1.3.1--h089eab3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 2e4985d20a8..c405c421a1b 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -3,7 +3,7 @@ process IVAR_VARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - def container_image = "/ivar:1.3.1--h089eab3_0" + def container_image = "/ivar:1.3.1--h089eab3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index fc4c2e0e977..35033df729e 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -8,7 +8,7 @@ process JUPYTERNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) - def container_image = "/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" + def container_image = "/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index 62568fdb033..747b280d48d 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -3,7 +3,7 @@ process KAIJU_KAIJU { label 'process_high' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - def container_image = "/kaiju:1.8.2--h5b5514e_1" + def container_image = "/kaiju:1.8.2--h5b5514e_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index e18cdaf1c27..58fe1496d58 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -3,7 +3,7 @@ process KAIJU_KAIJU2KRONA { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - def container_image = "/kaiju:1.8.2--h5b5514e_1" + def container_image = "/kaiju:1.8.2--h5b5514e_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 83bb1d9f776..e32a8da1111 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -3,7 +3,7 @@ process KAIJU_KAIJU2TABLE { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - def container_image = "/kaiju:1.8.2--h5b5514e_1" + def container_image = "/kaiju:1.8.2--h5b5514e_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 89af4c37c94..b98490e6639 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -3,7 +3,7 @@ process KALLISTO_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) - def container_image = "/kallisto:0.46.2--h4f7b962_1" + def container_image = "/kallisto:0.46.2--h4f7b962_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 9c564de2ab8..ef749679111 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -3,7 +3,7 @@ process KALLISTOBUSTOOLS_COUNT { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - def container_image = "/kb-python:0.27.2--pyhdfd78af_0" + def container_image = "/kb-python:0.27.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index c19bc847560..24cc1154d71 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -3,7 +3,7 @@ process KALLISTOBUSTOOLS_REF { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - def container_image = "/kb-python:0.27.2--pyhdfd78af_0" + def container_image = "/kb-python:0.27.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 42899368f18..75188917032 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -3,7 +3,7 @@ process KAT_HIST { label 'process_medium' conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) - def container_image = "/kat:2.4.2--py38hfc5f9d8_2" + def container_image = "/kat:2.4.2--py38hfc5f9d8_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index a9282a25187..faf991fef1a 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -3,7 +3,7 @@ process KHMER_NORMALIZEBYMEDIAN { label 'process_long' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - def container_image = "/khmer:3.0.0a3--py37haa7609a_2" + def container_image = "/khmer:3.0.0a3--py37haa7609a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 3dce00235a8..74bc1182f9f 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -3,7 +3,7 @@ process KHMER_UNIQUEKMERS { label 'process_low' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - def container_image = "/khmer:3.0.0a3--py37haa7609a_2" + def container_image = "/khmer:3.0.0a3--py37haa7609a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index 3f21fe2ac89..afec47d2b23 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -3,7 +3,7 @@ process KLEBORATE { label 'process_medium' conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) - def container_image = "/kleborate:2.1.0--pyhdfd78af_1" + def container_image = "/kleborate:2.1.0--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 8d8d7d6098b..28a94be9a13 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -3,7 +3,7 @@ process KRAKEN2_KRAKEN2 { label 'process_high' conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) - def container_image = "/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" + def container_image = "/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index 67ada0404c3..afe56201a88 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,8 +2,9 @@ process KRAKENTOOLS_COMBINEKREPORTS { label 'process_single' conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - def container_image = "/krakentools:1.2--pyh5e36f6f_0" + def container_image = "/krakentools:1.2--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index f99eed84d57..d9c7cfad61f 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -4,7 +4,7 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - def container_image = "/krakentools:1.2--pyh5e36f6f_0" + def container_image = "/krakentools:1.2--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index 18e0cc3fc67..ceb618035e0 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -4,7 +4,7 @@ process KRONA_KRONADB { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - def container_image = "/krona:2.7.1--pl526_5" + def container_image = "/krona:2.7.1--pl526_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 35320a35420..706cf9bf138 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -4,7 +4,7 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) - def container_image = "/krona:2.8--pl5262hdfd78af_2" + def container_image = "/krona:2.8--pl5262hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 82f14e80c0d..78655353618 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -3,7 +3,7 @@ process KRONA_KTIMPORTTEXT { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) - def container_image = "/krona:2.8.1--pl5321hdfd78af_1" + def container_image = "/krona:2.8.1--pl5321hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index 4d28c3f69ed..34b2dea3a03 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -4,7 +4,7 @@ process KRONA_KTUPDATETAXONOMY { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - def container_image = "/krona:2.7.1--pl526_5" + def container_image = "/krona:2.7.1--pl526_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 926f98bf717..7999fbd5a74 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -3,8 +3,9 @@ process LAST_DOTPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 9d8a7ec43db..767c35d32d4 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -3,7 +3,7 @@ process LAST_LASTAL { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index d78c98b59d4..ae602410baa 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -3,8 +3,9 @@ process LAST_LASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index e5343edb2d8..10a432ec2f3 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -3,7 +3,7 @@ process LAST_MAFCONVERT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 1154bbef0fe..f091dd3d377 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -3,7 +3,7 @@ process LAST_MAFSWAP { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 4eb6bd8ed0c..dc5e8af88cf 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -3,8 +3,9 @@ process LAST_POSTMASK { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 2320715a08d..09e4d2dbac6 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -3,8 +3,9 @@ process LAST_SPLIT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 5ba733380df..00aec540fcf 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -3,7 +3,7 @@ process LAST_TRAIN { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" + def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index 61555c08a15..680a2684908 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -4,7 +4,7 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) - def container_image = "/leehom:1.2.15--h29e30f7_1" + def container_image = "/leehom:1.2.15--h29e30f7_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index f6bf3c5e97c..a3ee06ec833 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -3,7 +3,7 @@ process LEGSTA { label 'process_medium' conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) - def container_image = "/legsta%3A0.5.1--hdfd78af_2" + def container_image = "/legsta%3A0.5.1--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 38be6fd3b72..f68781782c1 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -3,7 +3,7 @@ process LIMA { label 'process_low' conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) - def container_image = "/lima:2.2.0--h9ee0642_0" + def container_image = "/lima:2.2.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index eba913f814d..056f0425e66 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -3,8 +3,9 @@ process LISSERO { label 'process_low' conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) - def container_image = "/lissero:0.4.9--py_0" + def container_image = "/lissero:0.4.9--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index 920be422f3e..a621dfa26c3 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -3,7 +3,7 @@ process LOFREQ_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 9240bb2558a..49f5eb81d6c 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -3,7 +3,7 @@ process LOFREQ_CALLPARALLEL { label 'process_high' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index 382033ff247..39323b1bc71 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -3,7 +3,7 @@ process LOFREQ_FILTER { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 4103cc5984f..4e2b5945984 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -3,7 +3,7 @@ process LOFREQ_INDELQUAL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" + def container_image = "/lofreq:2.1.5--py38h588ecb2_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 2cfb7eb0498..1f6ff4338b4 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -3,7 +3,7 @@ process MACREL_CONTIGS { label 'process_medium' conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) - def container_image = "/macrel:1.1.0--py36hc5360cc_0" + def container_image = "/macrel:1.1.0--py36hc5360cc_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 4d1353a65ea..9f6b0d3ea12 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -3,7 +3,7 @@ process MACS2_CALLPEAK { label 'process_medium' conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) - def container_image = "/macs2:2.2.7.1--py38h4a8c8d9_3" + def container_image = "/macs2:2.2.7.1--py38h4a8c8d9_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 5bf73ad841c..a64a59f92ca 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -3,7 +3,7 @@ process MAFFT { label 'process_high' conda (params.enable_conda ? "bioconda::mafft=7.490" : null) - def container_image = "/mafft:7.490--h779adbc_0" + def container_image = "/mafft:7.490--h779adbc_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 2b83bdcbf79..6e671571b9b 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -3,7 +3,7 @@ process MALT_BUILD { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - def container_image = "/malt:0.41--1" + def container_image = "/malt:0.41--1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index a90e7cdc350..6e22ed77e3a 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -3,7 +3,7 @@ process MALT_RUN { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - def container_image = "/malt:0.41--1" + def container_image = "/malt:0.41--1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index ac5ff48acb3..2c506373e64 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -3,7 +3,7 @@ process MALTEXTRACT { label 'process_medium' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - def container_image = "/hops:0.35--hdfd78af_1" + def container_image = "/hops:0.35--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 5e627a7b55b..02f36af4e04 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -3,8 +3,9 @@ process MANTA_CONVERTINVERSION { label 'process_low' conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" + def container_image = "/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index e0f9061fc9b..3c6bea97519 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -3,8 +3,9 @@ process MANTA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - def container_image = "/manta:1.6.0--h9ee0642_1" + def container_image = "/manta:1.6.0--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 023071942e5..7b9c145bd42 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -3,8 +3,9 @@ process MANTA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - def container_image = "/manta:1.6.0--h9ee0642_1" + def container_image = "/manta:1.6.0--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index f0f671c09a7..b154e6a3363 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -3,8 +3,9 @@ process MANTA_TUMORONLY { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - def container_image = "/manta:1.6.0--h9ee0642_1" + def container_image = "/manta:1.6.0--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index 68a7364a470..928c77b5430 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -3,7 +3,7 @@ process MAPDAMAGE2 { label 'process_single' conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) - def container_image = "/mapdamage2:2.2.1--pyr40_0" + def container_image = "/mapdamage2:2.2.1--pyr40_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index f5abbc5459f..62c49d99a22 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -3,7 +3,7 @@ process MASH_DIST { label 'process_low' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - def container_image = "/mash:2.3--he348c14_1" + def container_image = "/mash:2.3--he348c14_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 083c39ae74e..970d8f581ef 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -3,7 +3,7 @@ process MASH_SCREEN { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - def container_image = "/mash:2.3--he348c14_1" + def container_image = "/mash:2.3--he348c14_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 6f7fb55c4c7..3c73caae75c 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -2,7 +2,7 @@ process MASH_SKETCH { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - def container_image = "/mash:2.3--he348c14_1" + def container_image = "/mash:2.3--he348c14_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index abdf86fca88..e28a310af8c 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -3,8 +3,9 @@ process MASHTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) - def container_image = "/mashtree:1.2.0--pl526h516909a_0" + def container_image = "/mashtree:1.2.0--pl526h516909a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 959007debf7..eb7f0d3f20e 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -3,7 +3,7 @@ process MAXBIN2 { label 'process_medium' conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) - def container_image = "/maxbin2:2.2.7--he1b5a44_2" + def container_image = "/maxbin2:2.2.7--he1b5a44_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index 012622008c6..b5466936ee9 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -4,7 +4,7 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) - def container_image = "/mcroni%3A1.0.4--pyh5e36f6f_0" + def container_image = "/mcroni%3A1.0.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index 0de119170ea..60c450bf0cb 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -3,7 +3,7 @@ process MD5SUM { label 'process_single' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - def container_image = "/ubuntu:20.04" + def container_image = "/ubuntu:20.04" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index f844450c1b9..c81adee639e 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -3,7 +3,7 @@ process MEDAKA { label 'process_high' conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) - def container_image = "/medaka:1.4.4--py38h130def0_0" + def container_image = "/medaka:1.4.4--py38h130def0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 029b6e7d399..18948cc136c 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -3,7 +3,7 @@ process MEGAHIT { label 'process_high' conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) - def container_image = "/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" + def container_image = "/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index cfedbfe66ee..f293e1ffa36 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -3,7 +3,7 @@ process MEGAN_DAA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - def container_image = "/megan:6.21.7--h9ee0642_0" + def container_image = "/megan:6.21.7--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index ec0883e31ef..32b4e892167 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -3,7 +3,7 @@ process MEGAN_RMA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - def container_image = "/megan:6.21.7--h9ee0642_0" + def container_image = "/megan:6.21.7--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index b1485d42999..619f9307f6f 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -3,8 +3,9 @@ process MENINGOTYPE { label 'process_low' conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) - def container_image = "/meningotype:0.8.5--pyhdfd78af_0" + def container_image = "/meningotype:0.8.5--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index dffe9aa4ef0..ab78fa8e484 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -3,7 +3,7 @@ process MERQURY { label 'process_low' conda (params.enable_conda ? "bioconda::merqury=1.3" : null) - def container_image = "/merqury:1.3--hdfd78af_1" + def container_image = "/merqury:1.3--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index 9eeaf3ca9bb..ece88013b4b 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -3,7 +3,7 @@ process MERYL_COUNT { label 'process_medium' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - def container_image = "/meryl:1.3--h87f3376_1" + def container_image = "/meryl:1.3--h87f3376_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 5a7409a8923..7b3c1198d27 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -3,7 +3,7 @@ process MERYL_HISTOGRAM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - def container_image = "/meryl:1.3--h87f3376_1" + def container_image = "/meryl:1.3--h87f3376_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 5fb6fc75002..37e6f2fdbf1 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -3,7 +3,7 @@ process MERYL_UNIONSUM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - def container_image = "/meryl:1.3--h87f3376_1" + def container_image = "/meryl:1.3--h87f3376_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index e017fdf9f68..64799adb018 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -3,7 +3,7 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - def container_image = "/metabat2:2.15--h986a166_1" + def container_image = "/metabat2:2.15--h986a166_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 384afd581cf..b59190ea0d9 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -3,7 +3,7 @@ process METABAT2_METABAT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - def container_image = "/metabat2:2.15--h986a166_1" + def container_image = "/metabat2:2.15--h986a166_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 40f2fd0d8b3..69db3e0be47 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,7 +2,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { label 'process_single' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" + def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 195528f521a..8f47737964f 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -3,7 +3,7 @@ process METAPHLAN3_METAPHLAN3 { label 'process_high' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" + def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 8c01f560450..7aeb848ae1d 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -3,7 +3,7 @@ process METHYLDACKEL_EXTRACT { label 'process_medium' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - def container_image = "/methyldackel:0.6.0--h22771d5_0" + def container_image = "/methyldackel:0.6.0--h22771d5_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index ad2c115a992..f8f001d4bef 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -3,7 +3,7 @@ process METHYLDACKEL_MBIAS { label 'process_low' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - def container_image = "/methyldackel:0.6.0--h22771d5_0" + def container_image = "/methyldackel:0.6.0--h22771d5_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 41bc183a9ff..5a13d41a732 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -3,7 +3,7 @@ process MINIA { label 'process_high' conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) - def container_image = "/minia:3.2.6--h9a82719_0" + def container_image = "/minia:3.2.6--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 0556ec038af..6a2acd52e2c 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -3,7 +3,7 @@ process MINIASM { label 'process_high' conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) - def container_image = "/miniasm:0.3_r179--h5bf99c6_2" + def container_image = "/miniasm:0.3_r179--h5bf99c6_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index 97b7fefcd74..ca0dc96e522 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -3,7 +3,7 @@ process MINIMAP2_ALIGN { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) - def container_image = "/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" + def container_image = "/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 1b78333e080..9a689e72971 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -2,7 +2,7 @@ process MINIMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) - def container_image = "/minimap2:2.21--h5bf99c6_0" + def container_image = "/minimap2:2.21--h5bf99c6_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 6344b098192..393b959025e 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -3,8 +3,9 @@ process MLST { label 'process_low' conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) - def container_image = "/mlst:2.19.0--hdfd78af_1" + def container_image = "/mlst:2.19.0--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index cef68878fee..2c5b48b8a4f 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -3,7 +3,7 @@ process MOBSUITE_RECON { label 'process_medium' conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) - def container_image = "/mob_suite%3A3.0.3--pyhdfd78af_0" + def container_image = "/mob_suite%3A3.0.3--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 34c432bab41..ee80fb8276b 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -3,7 +3,7 @@ process MOSDEPTH { label 'process_medium' conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) - def container_image = "/mosdepth:0.3.3--hdfd78af_1" + def container_image = "/mosdepth:0.3.3--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index 6a6d190f084..2a5c25cac4c 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -2,7 +2,7 @@ process MOTUS_DOWNLOADDB { label 'process_low' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - def container_image = "/motus:3.0.1--pyhdfd78af_0" + def container_image = "/motus:3.0.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 06fba27827c..075362bca68 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -5,7 +5,7 @@ process MOTUS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - def container_image = "/motus:3.0.1--pyhdfd78af_0" + def container_image = "/motus:3.0.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index e6ddaeed3d0..3b9ce2ac5fc 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -3,7 +3,7 @@ process MOTUS_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - def container_image = "/motus:3.0.1--pyhdfd78af_0" + def container_image = "/motus:3.0.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index a976f0de653..ab8659f35ec 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -3,7 +3,7 @@ process MSISENSOR_MSI { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - def container_image = "/msisensor:0.5--hb3646a4_2" + def container_image = "/msisensor:0.5--hb3646a4_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index 025f7ebe581..6adeb96538f 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -3,7 +3,7 @@ process MSISENSOR_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - def container_image = "/msisensor:0.5--hb3646a4_2" + def container_image = "/msisensor:0.5--hb3646a4_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index 72269350eef..69b5b28622d 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -3,7 +3,7 @@ process MSISENSOR2_MSI { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - def container_image = "/msisensor2:0.1--hd03093a_0" + def container_image = "/msisensor2:0.1--hd03093a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index 6c66181566e..f44ff3bb463 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -3,7 +3,7 @@ process MSISENSOR2_SCAN { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - def container_image = "/msisensor2:0.1--hd03093a_0" + def container_image = "/msisensor2:0.1--hd03093a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index 939798405cb..da124b8ba6f 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -3,7 +3,7 @@ process MSISENSORPRO_MSI_SOMATIC { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" + def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index 8086bf8e09a..a549999999c 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -3,7 +3,7 @@ process MSISENSORPRO_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" + def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index 5bb6ec2e204..14714850ef5 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -3,8 +3,9 @@ process MTNUCRATIO { label 'process_single' conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) - def container_image = "/mtnucratio:0.7--hdfd78af_2" + def container_image = "/mtnucratio:0.7--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 3bb99fd66ad..6cc80edff3e 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -2,8 +2,9 @@ process MULTIQC { label 'process_single' conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - def container_image = "/multiqc:1.13--pyhdfd78af_0" + def container_image = "/multiqc:1.13--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index ac345b622f3..3fa20d68ea3 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -3,8 +3,9 @@ process MULTIVCFANALYZER { label 'process_single' conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) - def container_image = "/multivcfanalyzer:0.85.2--hdfd78af_1" + def container_image = "/multivcfanalyzer:0.85.2--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path vcfs diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index f1210a0d492..4ecb10f2aaa 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -4,7 +4,7 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - def container_image = "/mummer:3.23--pl5262h1b792b2_12" + def container_image = "/mummer:3.23--pl5262h1b792b2_12" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 247c230dd3d..07c7cc087ad 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -3,7 +3,7 @@ process MUSCLE { label 'process_single' conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) - def container_image = "/muscle:3.8.1551--h7d875b9_6" + def container_image = "/muscle:3.8.1551--h7d875b9_6" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index 4f1e9349837..5d682d727d4 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -3,7 +3,7 @@ process MYKROBE_PREDICT { label 'process_low' conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) - def container_image = "/mykrobe:0.11.0--py39h2add14b_1" + def container_image = "/mykrobe:0.11.0--py39h2add14b_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 1fa24ec43da..66014fbd18c 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -3,8 +3,9 @@ process NANOLYSE { label 'process_low' conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) - def container_image = "/nanolyse:1.2.0--py_0" + def container_image = "/nanolyse:1.2.0--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index b184f01ede1..01fb5f33ed8 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -3,7 +3,7 @@ process NANOPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) - def container_image = "/nanoplot:1.40.0--pyhdfd78af_0" + def container_image = "/nanoplot:1.40.0--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index 06338c8363e..858ae2387de 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -3,7 +3,7 @@ process NCBIGENOMEDOWNLOAD { label 'process_low' conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) - def container_image = "/ncbi-genome-download:0.3.1--pyh5e36f6f_0" + def container_image = "/ncbi-genome-download:0.3.1--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 0ec1f7fe92e..03f2a8280a8 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -3,7 +3,7 @@ process NEXTCLADE_DATASETGET { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - def container_image = "/nextclade:2.2.0--h9ee0642_0" + def container_image = "/nextclade:2.2.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 751ebd74ad9..64496533c39 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -3,7 +3,7 @@ process NEXTCLADE_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - def container_image = "/nextclade:2.2.0--h9ee0642_0" + def container_image = "/nextclade:2.2.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index 73662d94103..0787e747ac7 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -3,7 +3,7 @@ process NEXTGENMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) - def container_image = "/nextgenmap%3A0.5.5--hc9558a2_4" + def container_image = "/nextgenmap%3A0.5.5--hc9558a2_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index 2b5c2d79979..718f99cb02e 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -3,7 +3,7 @@ process NGMASTER { label 'process_low' conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) - def container_image = "/ngmaster:0.5.8--pyhdfd78af_1" + def container_image = "/ngmaster:0.5.8--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 6ed78cc2d17..9d7944575a0 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,7 +2,7 @@ process NGSCHECKMATE_NCM { label 'process_low' conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) - def container_image = "/ngscheckmate:1.0.0--py27r41hdfd78af_3" + def container_image = "/ngscheckmate:1.0.0--py27r41hdfd78af_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index 8f7a49f9de5..c69b6ebb55f 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -3,7 +3,7 @@ process NUCMER { label 'process_low' conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - def container_image = "/mummer:3.23--pl5262h1b792b2_12" + def container_image = "/mummer:3.23--pl5262h1b792b2_12" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 62baee77e38..0b4ee308b04 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -3,7 +3,7 @@ process OPTITYPE { label 'process_medium' conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) - def container_image = "/optitype:1.3.5--0" + def container_image = "/optitype:1.3.5--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index 9da1cc9ba80..19dd2dc0846 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -3,7 +3,7 @@ process PAIRIX { label 'process_medium' conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) - def container_image = "/pairix:0.3.7--py36h30a8e3e_3" + def container_image = "/pairix:0.3.7--py36h30a8e3e_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 40b3cf014b8..e4fc4feab01 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -3,7 +3,7 @@ process PAIRTOOLS_DEDUP { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 8a85efca518..0c6805c4292 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_FLIP { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 8681cac60a2..f49f1881025 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -3,7 +3,7 @@ process PAIRTOOLS_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 5f2043fc083..1684e6d2936 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -3,7 +3,7 @@ process PAIRTOOLS_RESTRICT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index aa7b1c00533..67a566d9670 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -3,7 +3,7 @@ process PAIRTOOLS_SELECT { label 'process_medium' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index 36e40b87e03..0aa3db2c37f 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -3,7 +3,7 @@ process PAIRTOOLS_SORT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" + def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index cbf549a4bb2..3d9a013f76a 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -3,7 +3,7 @@ process PANAROO_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) - def container_image = "/panaroo:1.2.9--pyhdfd78af_0" + def container_image = "/panaroo:1.2.9--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 25e7a9d1068..8aa629eab8f 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -3,8 +3,9 @@ process PANGOLIN { label 'process_medium' conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) - def container_image = "/pangolin:4.1.1--pyhdfd78af_0" + def container_image = "/pangolin:4.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index 2705b9aa12e..8b90b62fe95 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -4,8 +4,9 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) - def container_image = "/paraclu:10--h9a82719_1" + def container_image = "/paraclu:10--h9a82719_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index bb4a29cc0c2..6936b1a7ce8 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -3,8 +3,9 @@ process PASTY { label 'process_single' conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) - def container_image = "/pasty:1.0.0--hdfd78af_0" + def container_image = "/pasty:1.0.0--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index 6894e728b58..0da8e9e174b 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -3,7 +3,7 @@ process PBBAM_PBMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) - def container_image = "/pbbam:1.7.0--h058f120_1" + def container_image = "/pbbam:1.7.0--h058f120_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 9701e9f7f42..d9ed988b69f 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -3,7 +3,7 @@ process PBCCS { label 'process_low' conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) - def container_image = "/pbccs:6.2.0--h9ee0642_0" + def container_image = "/pbccs:6.2.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index ffdc9826b13..28935b1295f 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -3,7 +3,7 @@ process PBPTYPER { label 'process_single' conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) - def container_image = "/pbptyper:1.0.2--hdfd78af_0" + def container_image = "/pbptyper:1.0.2--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index 1434bcb2673..b4a8ac39e1a 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -3,7 +3,7 @@ process PEAR { label 'process_low' conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) - def container_image = "/pear:0.9.6--h67092d7_8" + def container_image = "/pear:0.9.6--h67092d7_8" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index 05be7a16081..0f5344c671b 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -3,7 +3,7 @@ process PEDDY { label 'process_low' conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) - def container_image = "/peddy:0.4.8--pyh5e36f6f_0" + def container_image = "/peddy:0.4.8--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 7f3b0e72fd7..9998b800799 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -4,7 +4,7 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) - def container_image = "/phantompeakqualtools:1.2.2--0" + def container_image = "/phantompeakqualtools:1.2.2--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index b769da3c789..ab70a3b5ce4 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -3,8 +3,9 @@ process PHYLOFLASH { label 'process_medium' conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) - def container_image = "/phyloflash:3.4--hdfd78af_1" + def container_image = "/phyloflash:3.4--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 38386e1763f..5bd44aeb31f 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -3,7 +3,7 @@ process PICARD_ADDORREPLACEREADGROUPS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 73a5412bb57..786790038e1 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -3,7 +3,7 @@ process PICARD_CLEANSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 55ca27a5024..ed5092aca9d 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -3,7 +3,7 @@ process PICARD_COLLECTHSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 912882a258c..c19ea982ebb 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -3,7 +3,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index e1bdf495811..9d1a69bfa5e 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -3,7 +3,7 @@ process PICARD_COLLECTWGSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 82f87de9619..4585cf2c626 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -3,7 +3,7 @@ process PICARD_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index ae9226fa65e..6509b2604c4 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -3,7 +3,7 @@ process PICARD_CROSSCHECKFINGERPRINTS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index 24286f2cc60..e42b0501eda 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -3,7 +3,7 @@ process PICARD_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index c3f0afd601e..c68307d4cd4 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -3,7 +3,7 @@ process PICARD_FILTERSAMREADS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index bb2bdbdb647..edbe6c9c13e 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -3,7 +3,7 @@ process PICARD_FIXMATEINFORMATION { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 504abc0c5a4..06c178ccb2b 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -3,7 +3,7 @@ process PICARD_LIFTOVERVCF { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 24d98eeb6fe..6ada3065bb7 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -3,7 +3,7 @@ process PICARD_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 6d8c20ee847..b50fb3033e8 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -3,7 +3,7 @@ process PICARD_MERGESAMFILES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 4822a4646f6..3b4f76088e2 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -4,7 +4,7 @@ process PICARD_RENAMESAMPLEINVCF { label 'process_single' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 3ca2dea6fe8..e5048fd96a3 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -3,7 +3,7 @@ process PICARD_SORTSAM { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index d9ac24c78b6..7e39895e5a5 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -3,7 +3,7 @@ process PICARD_SORTVCF { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" + def container_image = "/picard:2.27.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index a95789f05e9..b6f4442c6c7 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -3,7 +3,7 @@ process PINTS_CALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) - def container_image = "/pypints:1.1.6--pyh5e36f6f_1" + def container_image = "/pypints:1.1.6--pyh5e36f6f_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index 8eeae528559..e875286daf4 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -3,7 +3,7 @@ process PIRATE { label 'process_medium' conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) - def container_image = "/pirate:1.0.4--hdfd78af_2" + def container_image = "/pirate:1.0.4--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index fc3836545fb..281f61edac4 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -4,7 +4,7 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) - def container_image = "/plasmidfinder:2.1.6--py310hdfd78af_1" + def container_image = "/plasmidfinder:2.1.6--py310hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index fca1218ff42..857739c5c23 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -3,7 +3,7 @@ process PLASMIDID { label 'process_medium' conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) - def container_image = "/plasmidid:1.6.5--hdfd78af_0" + def container_image = "/plasmidid:1.6.5--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index 1a07e26ee33..fdf98899e61 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -3,7 +3,7 @@ process PLINK_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - def container_image = "/plink:1.90b6.21--h779adbc_1" + def container_image = "/plink:1.90b6.21--h779adbc_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index 4db6dd05ad6..4a891f8eaeb 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -3,7 +3,7 @@ process PLINK_VCF { label 'process_medium' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - def container_image = "/plink:1.90b6.21--h779adbc_1" + def container_image = "/plink:1.90b6.21--h779adbc_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index 131a6102951..bd2abcf3725 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -3,7 +3,7 @@ process PLINK2_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - def container_image = "/plink2:2.00a2.3--h712d239_1" + def container_image = "/plink2:2.00a2.3--h712d239_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index d713330fe33..88d69810433 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -3,7 +3,7 @@ process PLINK2_SCORE { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - def container_image = "/plink2:2.00a2.3--h712d239_1" + def container_image = "/plink2:2.00a2.3--h712d239_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index a021613657f..e3c7e24693e 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -3,7 +3,7 @@ process PLINK2_VCF { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - def container_image = "/plink2:2.00a2.3--h712d239_1" + def container_image = "/plink2:2.00a2.3--h712d239_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 9f30b80aace..609408910da 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -3,7 +3,7 @@ process PMDTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) - def container_image = "/pmdtools:0.60--hdfd78af_5" + def container_image = "/pmdtools:0.60--hdfd78af_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index f19616720a7..6bfbf9c1982 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -3,7 +3,7 @@ process PORECHOP { label 'process_medium' conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) - def container_image = "/porechop:0.2.4--py39h7cff6ad_2" + def container_image = "/porechop:0.2.4--py39h7cff6ad_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 000eb3bc283..3df01db792a 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -4,7 +4,7 @@ process PRESEQ_CCURVE { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - def container_image = "/preseq:3.1.2--h445547b_2" + def container_image = "/preseq:3.1.2--h445547b_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index bcfd3ca8b51..38ca6912ec5 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -4,7 +4,7 @@ process PRESEQ_LCEXTRAP { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - def container_image = "/preseq:3.1.2--h445547b_2" + def container_image = "/preseq:3.1.2--h445547b_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index 4ee07a7ad2b..3e2618a5d57 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -3,7 +3,7 @@ process PRINSEQPLUSPLUS { label 'process_low' conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) - def container_image = "/prinseq-plus-plus:1.2.3--hc90279e_1" + def container_image = "/prinseq-plus-plus:1.2.3--hc90279e_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 8a44b7caded..114391e1dd4 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -3,8 +3,9 @@ process PRODIGAL { label 'process_single' conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) - def container_image = "/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" + def container_image = "/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 2291cb3e282..1d4085f2280 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -3,7 +3,7 @@ process PROKKA { label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) - def container_image = "/prokka%3A1.14.6--pl5321hdfd78af_4" + def container_image = "/prokka%3A1.14.6--pl5321hdfd78af_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index ad1d050de10..fe1ad718090 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -3,7 +3,7 @@ process PYCOQC { label 'process_medium' conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) - def container_image = "/pycoqc:2.5.2--py_0" + def container_image = "/pycoqc:2.5.2--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index 87755d80993..ecda2a3b46f 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -3,7 +3,7 @@ process PYDAMAGE_ANALYZE { label 'process_medium' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - def container_image = "/pydamage:0.70--pyhdfd78af_0" + def container_image = "/pydamage:0.70--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index ca9b67ecf9e..1a8be87ec58 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -3,7 +3,7 @@ process PYDAMAGE_FILTER { label 'process_single' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - def container_image = "/pydamage:0.70--pyhdfd78af_0" + def container_image = "/pydamage:0.70--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 125f8fc4488..e13a85ea201 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -3,7 +3,7 @@ process QCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) - def container_image = "/qcat:1.1.0--py_0" + def container_image = "/qcat:1.1.0--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 3c28c8c1b8d..9d2c9c0534b 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -3,7 +3,7 @@ process QUALIMAP_BAMQC { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - def container_image = "/qualimap:2.2.2d--1" + def container_image = "/qualimap:2.2.2d--1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 1a527bed414..0dc68fd70bc 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -3,7 +3,7 @@ process QUALIMAP_BAMQCCRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" + def container_image = "/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index b783c66991a..73d0392e1c0 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -3,7 +3,7 @@ process QUALIMAP_RNASEQ { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - def container_image = "/qualimap:2.2.2d--1" + def container_image = "/qualimap:2.2.2d--1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index 35139a2b2bb..d7bb08ef288 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -2,7 +2,7 @@ process QUAST { label 'process_medium' conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) - def container_image = "/quast:5.2.0--py39pl5321h2add14b_1" + def container_image = "/quast:5.2.0--py39pl5321h2add14b_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index f6fd985feca..d1b62b2bf79 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -3,7 +3,7 @@ process RACON { label 'process_high' conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) - def container_image = "/racon:1.4.20--h9a82719_1" + def container_image = "/racon:1.4.20--h9a82719_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 8513c29eaaa..6fb5f8db687 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -3,8 +3,9 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) - def container_image = "/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" + def container_image = "/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 79a015f06c9..a24fe59ecb4 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -3,7 +3,7 @@ process RASUSA { label 'process_low' conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) - def container_image = "/rasusa:0.3.0--h779adbc_1" + def container_image = "/rasusa:0.3.0--h779adbc_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index 788dfb3226f..c6ae348516d 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -3,7 +3,7 @@ process RAVEN { label 'process_medium' conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) - def container_image = "/raven-assembler:1.6.1--h2e03b76_0" + def container_image = "/raven-assembler:1.6.1--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index 4ea5ad556f8..ddbbb45e159 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -2,7 +2,7 @@ process RAXMLNG { label 'process_high' conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) - def container_image = "/raxml-ng:1.0.3--h32fcf60_0" + def container_image = "/raxml-ng:1.0.3--h32fcf60_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 467c875f0ac..db4ad2edf9f 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -3,7 +3,7 @@ process RGI_MAIN { label 'process_medium' conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) - def container_image = "/rgi:5.2.1--pyha8f3691_2" + def container_image = "/rgi:5.2.1--pyha8f3691_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 596e6bca22e..6098705fe71 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -3,8 +3,9 @@ process RHOCALL_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) - def container_image = "/rhocall:0.5.1--py39hbf8eff0_0" + def container_image = "/rhocall:0.5.1--py39hbf8eff0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index da6fa88bd94..719b3f016d0 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -8,7 +8,7 @@ process RMARKDOWNNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) - def container_image = "/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" + def container_image = "/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index 6dd473c5b9b..c1816e15dd8 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -3,7 +3,7 @@ process ROARY { label 'process_medium' conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) - def container_image = "/roary:3.13.0--pl526h516909a_0" + def container_image = "/roary:3.13.0--pl526h516909a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 6e21a6fa3d2..ba22da6d381 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -3,7 +3,7 @@ process RSEM_CALCULATEEXPRESSION { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" + def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 18e84bfc76c..56b20bdf1bc 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -3,7 +3,7 @@ process RSEM_PREPAREREFERENCE { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" + def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index 67219602172..e8ba91135b2 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -3,7 +3,7 @@ process RSEQC_BAMSTAT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index c434d67f86a..32834be468e 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -3,7 +3,7 @@ process RSEQC_INFEREXPERIMENT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index e6322737868..cf03eaeaf1d 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -3,7 +3,7 @@ process RSEQC_INNERDISTANCE { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index 96ef7827a50..f2a4efb0716 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -3,7 +3,7 @@ process RSEQC_JUNCTIONANNOTATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 07041cdc19c..128cd204c66 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -3,7 +3,7 @@ process RSEQC_JUNCTIONSATURATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index 701f9343aac..98b0f02febe 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -3,7 +3,7 @@ process RSEQC_READDISTRIBUTION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 055e6695983..61949337a7b 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -3,7 +3,7 @@ process RSEQC_READDUPLICATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 4b286d1b908..3866400af5c 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -3,7 +3,7 @@ process RSEQC_TIN { label 'process_high' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" + def container_image = "/rseqc:3.0.1--py37h516909a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 52bbb6e0573..7a0d68cf700 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -3,7 +3,7 @@ process RTGTOOLS_PEDFILTER { label 'process_low' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - def container_image = "/rtg-tools:3.12.1--hdfd78af_0" + def container_image = "/rtg-tools:3.12.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index d6ee5576070..ed83c042e07 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -3,7 +3,7 @@ process RTGTOOLS_VCFEVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - def container_image = "/rtg-tools:3.12.1--hdfd78af_0" + def container_image = "/rtg-tools:3.12.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index c8292099e4d..a0a58ecf773 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -3,7 +3,7 @@ process SALMON_INDEX { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - def container_image = "/salmon:1.5.2--h84f40af_0" + def container_image = "/salmon:1.5.2--h84f40af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 7e867c806b0..f8ef268682a 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -3,7 +3,7 @@ process SALMON_QUANT { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - def container_image = "/salmon:1.5.2--h84f40af_0" + def container_image = "/salmon:1.5.2--h84f40af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 3e1a7c52d6b..6160226df87 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -3,7 +3,7 @@ process SAMBLASTER { label 'process_low' conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" + def container_image = "/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 454289fa14f..f82be398f76 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_AMPLICONCLIP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index c0ca12b9bac..82907463fc2 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_BAM2FQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 261629b41f1..3d88d3c6940 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_COLLATE { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 887734e6065..3631069fdd4 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_COLLATEFASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index b27c0475e2b..0aa10559505 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 91b45defba8..3a7424fe2fc 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_DEPTH { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 304600d122f..9975271a78c 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_DICT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index bd19f7a4acc..d61a38cf67b 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_FAIDX { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 6cc3e380243..186b59e0b03 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_FASTA { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 2fe687462c5..2afbbef0b31 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_FASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 481ca22e3b1..6e85fab7c70 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_FIXMATE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 972772d4af3..84f866ae5a0 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_FLAGSTAT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 18163e13d77..aa054eff8b6 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_GETRG { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 034eb4a2e49..24f8ddc3a7d 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_IDXSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index be48bc0acfa..6da574867a9 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index b9c4cfb6c5a..473e5ebd726 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_MARKDUP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 8cd2247c305..71efca897ec 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index ba5542a41ee..d9e9d8ffab6 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_MPILEUP { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(intervals) diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index dd78f242b93..e2aeb48080d 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 88d912c397e..406016bafc3 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 81ada981f9e..db26333be22 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -3,7 +3,7 @@ process SAMTOOLS_VIEW { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" + def container_image = "/samtools:1.15.1--h1170115_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index df08efc136d..afcfe794652 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -3,8 +3,9 @@ process SCOARY { label 'process_low' conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) - def container_image = "/scoary:1.6.16--py_2" + def container_image = "/scoary:1.6.16--py_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index 4a874a738a8..7307ad93f97 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -3,7 +3,7 @@ process SCRAMBLE_CLUSTERANALYSIS { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - def container_image = "/scramble:1.0.1--h779adbc_1" + def container_image = "/scramble:1.0.1--h779adbc_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 9c30ea89b20..88f00cd761d 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -3,7 +3,7 @@ process SCRAMBLE_CLUSTERIDENTIFIER { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - def container_image = "/scramble:1.0.1--h779adbc_1" + def container_image = "/scramble:1.0.1--h779adbc_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index f81d7bff98d..b26f6b81c90 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -4,7 +4,7 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) - def container_image = "/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" + def container_image = "/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index f8d1942d68e..90bb690350b 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -3,7 +3,7 @@ process SEQKIT_PAIR { label 'process_medium' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - def container_image = "/seqkit:2.1.0--h9ee0642_0" + def container_image = "/seqkit:2.1.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index 7672deb33ae..c13542b4ff2 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -3,7 +3,7 @@ process SEQKIT_REPLACE { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - def container_image = "/seqkit:2.1.0--h9ee0642_0" + def container_image = "/seqkit:2.1.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index 0f97d32400e..fdd80164917 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -3,7 +3,7 @@ process SEQKIT_SPLIT2 { label 'process_medium' conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) - def container_image = "/seqkit:2.1.0--h9ee0642_0" + def container_image = "/seqkit:2.1.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index a2e83e68b39..f00abcaf52e 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -3,7 +3,7 @@ process SEQKIT_STATS { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) - def container_image = "/seqkit:2.2.0--h9ee0642_0" + def container_image = "/seqkit:2.2.0--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index e8c8d7bc153..771bd2725bf 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -3,7 +3,7 @@ process SEQSERO2 { label 'process_low' conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) - def container_image = "/seqsero2:1.2.1--py_0" + def container_image = "/seqsero2:1.2.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 7a21f267ffa..ebdf56c0d97 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -3,7 +3,7 @@ process SEQTK_MERGEPE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" + def container_image = "/seqtk:1.3--h5bf99c6_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index ed852c75b24..b0f0864124a 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -3,7 +3,7 @@ process SEQTK_RENAME { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" + def container_image = "/seqtk:1.3--h5bf99c6_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index e6036501713..c2b5d6bd2b2 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -3,7 +3,7 @@ process SEQTK_SAMPLE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" + def container_image = "/seqtk:1.3--h5bf99c6_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 307bf12204d..9258458bb1d 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -3,7 +3,7 @@ process SEQTK_SEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" + def container_image = "/seqtk:1.3--h5bf99c6_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 829aefaac33..d8c1cf66342 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -3,7 +3,7 @@ process SEQTK_SUBSEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" + def container_image = "/seqtk:1.3--h5bf99c6_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index 368c9612173..87fb4117ac1 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -3,7 +3,7 @@ process SEQUENZAUTILS_BAM2SEQZ { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" + def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 070fa9e5ade..c48af9cc868 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -3,7 +3,7 @@ process SEQUENZAUTILS_GCWIGGLE { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" + def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 7a906954d7a..64af395c40e 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -4,7 +4,7 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) - def container_image = "/seqwish:0.7.6--h5b5514e_1" + def container_image = "/seqwish:0.7.6--h5b5514e_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 4fe940491d5..d94c260766e 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -3,7 +3,7 @@ process SEROBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) - def container_image = "/seroba:1.0.2--pyhdfd78af_1" + def container_image = "/seroba:1.0.2--pyhdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index d50906a28de..7db08d4ac6d 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -3,7 +3,7 @@ process SEXDETERRMINE { label 'process_single' conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) - def container_image = "/sexdeterrmine:1.1.2--hdfd78af_1" + def container_image = "/sexdeterrmine:1.1.2--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 0667eed6260..6e09ce900fa 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -3,7 +3,7 @@ process SHASTA { label 'process_medium' conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) - def container_image = "/shasta:0.8.0--h7d875b9_0" + def container_image = "/shasta:0.8.0--h7d875b9_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index e330077d27a..80ce221969f 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -3,7 +3,7 @@ process SHASUM { label 'process_low' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - def container_image = "/ubuntu:20.04" + def container_image = "/ubuntu:20.04" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index 8f531253cd3..b21aaed75eb 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -3,7 +3,7 @@ process SHIGATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) - def container_image = "/shigatyper%3A2.0.1--pyhdfd78af_0" + def container_image = "/shigatyper%3A2.0.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 60ab0f21eb9..9839298c414 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -3,7 +3,7 @@ process SHOVILL { label 'process_medium' conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) - def container_image = "/shovill:1.1.0--0" + def container_image = "/shovill:1.1.0--0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 09655f019a3..9f2e5c5ea33 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -3,8 +3,9 @@ process SISTR { label 'process_medium' conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) - def container_image = "/sistr_cmd:1.1.1--pyh864c0ab_2" + def container_image = "/sistr_cmd:1.1.1--pyh864c0ab_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 45a8cbee0ea..19160de8fbe 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -4,7 +4,7 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) - def container_image = "/slimfastq:2.04--h87f3376_2" + def container_image = "/slimfastq:2.04--h87f3376_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index 27955baf1a5..d4423e66006 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -3,7 +3,7 @@ process SNAPALIGNER_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - def container_image = "/snap-aligner:2.0.1--hd03093a_1" + def container_image = "/snap-aligner:2.0.1--hd03093a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index 1b799179c4c..cd9e63dd7c7 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -3,7 +3,7 @@ process SNAPALIGNER_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - def container_image = "/snap-aligner:2.0.1--hd03093a_1" + def container_image = "/snap-aligner:2.0.1--hd03093a_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index b0596591f40..033b1236275 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -3,7 +3,7 @@ process SNIPPY_CORE { label 'process_medium' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - def container_image = "/snippy:4.6.0--hdfd78af_2" + def container_image = "/snippy:4.6.0--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index eebe1257b90..a86b8f215f9 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -3,7 +3,7 @@ process SNIPPY_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - def container_image = "/snippy:4.6.0--hdfd78af_2" + def container_image = "/snippy:4.6.0--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 689161224ca..7d2dcb79dd0 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -3,7 +3,7 @@ process SNPDISTS { label 'process_low' conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) - def container_image = "/snp-dists:0.8.2--h5bf99c6_0" + def container_image = "/snp-dists:0.8.2--h5bf99c6_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 56bfc4f1f08..2eac6019a32 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -3,7 +3,7 @@ process SNPEFF { label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) - def container_image = "/snpeff:5.1--hdfd78af_2" + def container_image = "/snpeff:5.1--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index 57c28a9eb25..9747d394831 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -3,8 +3,9 @@ process SNPSIFT_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) - def container_image = "/snpsift:4.3.1t--hdfd78af_3" + def container_image = "/snpsift:4.3.1t--hdfd78af_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index 4713a43ec28..a1b3258e2f8 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -2,8 +2,9 @@ process SNPSITES { label 'process_medium' conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) - def container_image = "/snp-sites:2.5.1--hed695b0_0" + def container_image = "/snp-sites:2.5.1--hed695b0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 3b5d90b41e9..9663d1e6adb 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -4,7 +4,7 @@ process SOMALIER_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - def container_image = "/somalier:0.2.15--h37c5b7d_0" + def container_image = "/somalier:0.2.15--h37c5b7d_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index 03da2d04b9b..1a5ac8f59db 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -4,7 +4,7 @@ process SOMALIER_RELATE { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - def container_image = "/somalier:0.2.15--h37c5b7d_0" + def container_image = "/somalier:0.2.15--h37c5b7d_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index f0a2976a530..3b42d05d8d8 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,7 +3,7 @@ process SORTMERNA { label "process_high" conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) - def container_image = "/sortmerna:4.3.4--h9ee0642_0" + def container_image = "/sortmerna:4.3.4--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index 64d08edaa36..7f9643f37a3 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -3,7 +3,7 @@ process SOURMASH_SKETCH { label 'process_low' conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) - def container_image = "/sourmash:4.2.4--hdfd78af_0" + def container_image = "/sourmash:4.2.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 11285ac5bb8..4cb65780033 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -3,7 +3,7 @@ process SPADES { label 'process_high' conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) - def container_image = "/spades:3.15.4--h95f258a_0" + def container_image = "/spades:3.15.4--h95f258a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index 887c12bc75a..5dbadb31333 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -3,7 +3,7 @@ process SPATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) - def container_image = "/spatyper:0.3.3--pyhdfd78af_3" + def container_image = "/spatyper:0.3.3--pyhdfd78af_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index 53b2934f48d..cfa2d728eff 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -3,7 +3,7 @@ process SRATOOLS_FASTERQDUMP { label 'process_medium' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) - def container_image = "/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" + def container_image = "/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 840ff37cc43..7a041b188ba 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -3,7 +3,7 @@ process SRATOOLS_PREFETCH { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" + def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index e90a4c8fbe6..1263d4022a7 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -3,7 +3,7 @@ process SRST2_SRST2 { label 'process_low' conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) - def container_image = "/srst2%3A0.2.0--py27_2" + def container_image = "/srst2%3A0.2.0--py27_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index d51c0770f9b..4e445393dea 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -4,7 +4,7 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) - def container_image = "/ssuissero%3A1.0.1--hdfd78af_0" + def container_image = "/ssuissero%3A1.0.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index a7a37d34a96..61d9cfa5cd9 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -3,7 +3,7 @@ process STADENIOLIB_SCRAMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) - def container_image = "/staden_io_lib:1.14.14--h0d9da7e_3" + def container_image = "/staden_io_lib:1.14.14--h0d9da7e_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index 3508f21e7e3..49c6a1eb6a3 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -3,8 +3,9 @@ process STAPHOPIASCCMEC { label 'process_low' conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) - def container_image = "/staphopia-sccmec:1.0.0--hdfd78af_0" + def container_image = "/staphopia-sccmec:1.0.0--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index bd176f83b3e..a9c9484d1b5 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,7 +3,7 @@ process STAR_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" + def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 27d734cff23..a32ad2d1a2c 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,7 +3,7 @@ process STAR_GENOMEGENERATE { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" + def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 73643112452..61be16073fb 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -3,7 +3,7 @@ process STRANGER { label 'process_low' conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) - def container_image = "/stranger:0.8.1--pyh5e36f6f_0" + def container_image = "/stranger:0.8.1--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 23b59638ed6..24e4d4caf7c 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -3,7 +3,7 @@ process STRELKA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - def container_image = "/strelka:2.9.10--h9ee0642_1" + def container_image = "/strelka:2.9.10--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 8bd62b9bb35..a8fae6ff4dc 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -3,7 +3,7 @@ process STRELKA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - def container_image = "/strelka:2.9.10--h9ee0642_1" + def container_image = "/strelka:2.9.10--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 9fab02f01d7..08a245c635a 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -3,7 +3,7 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - def container_image = "/stringtie:2.2.1--hecb563c_2" + def container_image = "/stringtie:2.2.1--hecb563c_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index eebde511543..22013c2928e 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -3,8 +3,9 @@ process STRINGTIE_STRINGTIE { label 'process_medium' conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - def container_image = "/stringtie:2.2.1--hecb563c_2" + def container_image = "/stringtie:2.2.1--hecb563c_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 443aa0edb5c..34180fcaa27 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -3,8 +3,9 @@ process SUBREAD_FEATURECOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) - def container_image = "/subread:2.0.1--hed695b0_0" + def container_image = "/subread:2.0.1--hed695b0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index fb12c07079f..2ab7b7d7f10 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -2,7 +2,7 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" + def container_image = "/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 3be936d62c2..8dc5ac01c14 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -3,7 +3,7 @@ process SVDB_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) - def container_image = "/svdb:2.6.1--py39h5371cbf_0" + def container_image = "/svdb:2.6.1--py39h5371cbf_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index 804c4a91bf4..f45b50e7abc 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -3,7 +3,7 @@ process SVTK_STANDARDIZE { label 'process_low' conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) - def container_image = "/svtk:0.0.20190615--py37h73a75cf_2" + def container_image = "/svtk:0.0.20190615--py37h73a75cf_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 0e7f67bcad3..efc3884d3f9 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -3,7 +3,7 @@ process TABIX_BGZIPTABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - def container_image = "/tabix:1.11--hdfd78af_0" + def container_image = "/tabix:1.11--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index b1eb6e1637a..0a2327f37d9 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -3,7 +3,7 @@ process TABIX_TABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - def container_image = "/tabix:1.11--hdfd78af_0" + def container_image = "/tabix:1.11--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 69c1ff27684..4a2639fe65b 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -3,7 +3,7 @@ process TAILFINDR { label 'process_high' conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) - def container_image = "/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" + def container_image = "/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index 9dc73d53f9c..7b6b4972a9a 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -3,7 +3,7 @@ process TBPROFILER_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) - def container_image = "/tb-profiler:3.0.8--pypyh5e36f6f_0" + def container_image = "/tb-profiler:3.0.8--pypyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 7b5f912061b..fc7569a095a 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -3,7 +3,7 @@ process TIDDIT_COV { label 'process_low' conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) - def container_image = "/tiddit:3.0.0--py39h59fae87_1" + def container_image = "/tiddit:3.0.0--py39h59fae87_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 9082419dfec..c5646341463 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -3,7 +3,7 @@ process TIDDIT_SV { label 'process_medium' conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) - def container_image = "/tiddit:3.1.0--py39h59fae87_1" + def container_image = "/tiddit:3.1.0--py39h59fae87_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index efaa44a9a3e..18475afe6ac 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -3,7 +3,7 @@ process TRANSDECODER_LONGORF { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" +def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index 266028d887f..2b3b6f429dd 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -3,7 +3,7 @@ process TRANSDECODER_PREDICT { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" + def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 3a532e02968..1a821563fd4 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -3,8 +3,9 @@ process TRIMGALORE { label 'process_high' conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) - def container_image = "/trim-galore:0.6.7--hdfd78af_0" + def container_image = "/trim-galore:0.6.7--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index a1a72803aa0..da5d1203d14 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -3,7 +3,7 @@ process TRIMMOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) - def container_image = "/trimmomatic:0.39--hdfd78af_2" + def container_image = "/trimmomatic:0.39--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index af547be54ab..d94fc793afb 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -4,7 +4,7 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) - def container_image = "/ucsc-bedclip:377--h0b8a92a_2" + def container_image = "/ucsc-bedclip:377--h0b8a92a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index f5e04c36204..867200882fc 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -4,7 +4,7 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) - def container_image = "/ucsc-bedgraphtobigwig:377--h446ed27_1" + def container_image = "/ucsc-bedgraphtobigwig:377--h446ed27_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index 9d8a09a952b..ddb22f54199 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -4,7 +4,7 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) - def container_image = "/ucsc-bedtobigbed:377--ha8a8165_3" + def container_image = "/ucsc-bedtobigbed:377--ha8a8165_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index 749d7ae1c1b..48cd17b08ee 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -4,7 +4,7 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) - def container_image = "/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" + def container_image = "/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index e7b650c8471..c6f37acd3a1 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -4,7 +4,7 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) - def container_image = "/ucsc-liftover:377--h0b8a92a_3" + def container_image = "/ucsc-liftover:377--h0b8a92a_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index c87602b7aac..5897831adbe 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -4,7 +4,7 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) - def container_image = "/ucsc-wigtobigwig:377--h0b8a92a_2" + def container_image = "/ucsc-wigtobigwig:377--h0b8a92a_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index d332bb6a4e7..8fa09e07656 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -3,7 +3,7 @@ process ULTRA_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" + def container_image = "/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 6801d6e36d6..33ba2d3525c 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -3,7 +3,7 @@ process ULTRA_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) - def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" + def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index 65a02ad0ae6..5f3db8c1fd1 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -3,7 +3,7 @@ process ULTRA_PIPELINE { label 'process_high' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) - def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" + def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 716ab3a2a7a..6fa32e49619 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -3,7 +3,7 @@ process UMITOOLS_DEDUP { label "process_medium" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" + def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 20286880cc3..67bf2804746 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -3,7 +3,7 @@ process UMITOOLS_EXTRACT { label "process_low" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" + def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index a61e75b0e99..4f4767ef0aa 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -3,7 +3,7 @@ process UNICYCLER { label 'process_high' conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) - def container_image = "/unicycler:0.4.8--py38h8162308_3" + def container_image = "/unicycler:0.4.8--py38h8162308_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 73bacd4d5d2..88fe0838849 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -3,8 +3,9 @@ process UNTAR { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - def container_image = "/ubuntu:20.04" + def container_image = "/ubuntu:20.04" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 401e0f6bd5e..b616f7bb482 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -3,8 +3,9 @@ process UNZIP { label 'process_single' conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) - def container_image = "/p7zip:15.09--h2d50403_4" + def container_image = "/p7zip:15.09--h2d50403_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 90f9e609547..940a976318b 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -3,7 +3,7 @@ process VARDICTJAVA { label 'process_medium' conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) - def container_image = "/vardict-java:1.8.3--hdfd78af_0" + def container_image = "/vardict-java:1.8.3--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index f02ebb6b42d..89585f76941 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -4,7 +4,7 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) - def container_image = "/variantbam:1.4.4a--h7d7f7ad_5" + def container_image = "/variantbam:1.4.4a--h7d7f7ad_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 5cd5613f08e..9f839252dec 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,7 +4,7 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) - def container_image = "/vcf2db:2020.02.24--hdfd78af_1" + def container_image = "/vcf2db:2020.02.24--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 098b9f00d1c..4d1d8b1e24b 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -5,7 +5,7 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) - def container_image = "/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" + def container_image = "/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index dd55cb39ff7..6ef6bc7f40e 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -3,8 +3,9 @@ process VCFANNO { label 'process_low' conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) - def container_image = "/vcfanno:0.3.3--h9ee0642_0" + def container_image = "/vcfanno:0.3.3--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 8e7b5b93d04..de179d4af17 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -3,7 +3,7 @@ process VCFLIB_VCFBREAKMULTI { label 'process_low' conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - def container_image = "/vcflib:1.0.3--hecb563c_1" + def container_image = "/vcflib:1.0.3--hecb563c_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index b620a759376..a199d3a0990 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -4,7 +4,7 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - def container_image = "/vcflib:1.0.3--hecb563c_1" + def container_image = "/vcflib:1.0.3--hecb563c_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index ff0b12ac1be..affbf58b251 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -3,7 +3,7 @@ process VCFTOOLS { label 'process_single' conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) - def container_image = "/vcftools:0.1.16--he513fc3_4" + def container_image = "/vcftools:0.1.16--he513fc3_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 07edd9543b2..2d94bba1615 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,7 +3,7 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) - def container_image = "/verifybamid2:2.0.1--hbb20b25_6" + def container_image = "/verifybamid2:2.0.1--hbb20b25_6" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index a11cfa380ab..82e863fbf7a 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -3,7 +3,7 @@ process VSEARCH_SINTAX { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - def container_image = "/vsearch:2.21.1--h95f258a_0" + def container_image = "/vsearch:2.21.1--h95f258a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index 67411a81a9f..b1d8577afe4 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -3,7 +3,7 @@ process VSEARCH_USEARCHGLOBAL { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - def container_image = "/vsearch:2.21.1--h95f258a_0" + def container_image = "/vsearch:2.21.1--h95f258a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index e122c5db66e..6a7dd67e1f1 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -3,7 +3,7 @@ process WGSIM { label 'process_medium' conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) - def container_image = "/wgsim:1.0--h5bf99c6_4" + def container_image = "/wgsim:1.0--h5bf99c6_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index f618397a612..522712e4d4c 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -3,7 +3,7 @@ process WHAMG { label 'process_medium' conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) - def container_image = "/wham:1.8.0.1.2017.05.03--h8b12597_1" + def container_image = "/wham:1.8.0.1.2017.05.03--h8b12597_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index 1a4db5136a4..b5997edc512 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -3,8 +3,9 @@ process YARA_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) - def container_image = "/yara:1.0.2--2" + def container_image = "/yara:1.0.2--2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index ff6a0507db5..90af0e7c579 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -3,8 +3,9 @@ process YARA_MAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" + def container_image = "/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } +n input: tuple val(meta), path(reads) From b9366bb7720e7ea3edd2143d611920205c1ccdd7 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 18:40:08 +0200 Subject: [PATCH 18/21] style: Fix container indentation --- modules/nf-core/abacas/main.nf | 2 +- modules/nf-core/abricate/run/main.nf | 2 +- modules/nf-core/abricate/summary/main.nf | 2 +- modules/nf-core/adapterremoval/main.nf | 2 +- modules/nf-core/adapterremovalfixprefix/main.nf | 2 +- modules/nf-core/agrvate/main.nf | 2 +- modules/nf-core/allelecounter/main.nf | 2 +- modules/nf-core/ampir/main.nf | 2 +- modules/nf-core/amplify/predict/main.nf | 2 +- modules/nf-core/amps/main.nf | 2 +- modules/nf-core/amrfinderplus/run/main.nf | 2 +- modules/nf-core/amrfinderplus/update/main.nf | 2 +- modules/nf-core/angsd/docounts/main.nf | 2 +- modules/nf-core/antismash/antismashlite/main.nf | 2 +- .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 2 +- modules/nf-core/aria2/main.nf | 2 +- modules/nf-core/ariba/getref/main.nf | 2 +- modules/nf-core/ariba/run/main.nf | 2 +- modules/nf-core/arriba/main.nf | 2 +- modules/nf-core/artic/guppyplex/main.nf | 2 +- modules/nf-core/artic/minion/main.nf | 2 +- modules/nf-core/ascat/main.nf | 2 +- modules/nf-core/assemblyscan/main.nf | 2 +- modules/nf-core/ataqv/ataqv/main.nf | 2 +- modules/nf-core/ataqv/mkarv/main.nf | 2 +- modules/nf-core/atlas/call/main.nf | 2 +- modules/nf-core/atlas/pmd/main.nf | 2 +- modules/nf-core/atlas/recal/main.nf | 2 +- modules/nf-core/atlas/splitmerge/main.nf | 2 +- modules/nf-core/bakta/main.nf | 2 +- modules/nf-core/bamaligncleaner/main.nf | 2 +- modules/nf-core/bamcmp/main.nf | 2 +- modules/nf-core/bamtools/convert/main.nf | 2 +- modules/nf-core/bamtools/split/main.nf | 2 +- modules/nf-core/bamtools/stats/main.nf | 2 +- modules/nf-core/bamutil/trimbam/main.nf | 2 +- modules/nf-core/bandage/image/main.nf | 2 +- modules/nf-core/bbmap/align/main.nf | 2 +- modules/nf-core/bbmap/bbduk/main.nf | 2 +- modules/nf-core/bbmap/bbsplit/main.nf | 2 +- modules/nf-core/bbmap/clumpify/main.nf | 2 +- modules/nf-core/bbmap/index/main.nf | 2 +- modules/nf-core/bbmap/pileup/main.nf | 2 +- modules/nf-core/bcftools/annotate/main.nf | 2 +- modules/nf-core/bcftools/concat/main.nf | 2 +- modules/nf-core/bcftools/consensus/main.nf | 2 +- modules/nf-core/bcftools/convert/main.nf | 2 +- modules/nf-core/bcftools/filter/main.nf | 2 +- modules/nf-core/bcftools/index/main.nf | 2 +- modules/nf-core/bcftools/isec/main.nf | 2 +- modules/nf-core/bcftools/merge/main.nf | 2 +- modules/nf-core/bcftools/mpileup/main.nf | 2 +- modules/nf-core/bcftools/norm/main.nf | 2 +- modules/nf-core/bcftools/query/main.nf | 2 +- modules/nf-core/bcftools/reheader/main.nf | 2 +- modules/nf-core/bcftools/roh/main.nf | 2 +- modules/nf-core/bcftools/sort/main.nf | 2 +- modules/nf-core/bcftools/stats/main.nf | 2 +- modules/nf-core/bcftools/view/main.nf | 2 +- modules/nf-core/bedtools/bamtobed/main.nf | 2 +- modules/nf-core/bedtools/complement/main.nf | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/bedtools/getfasta/main.nf | 2 +- modules/nf-core/bedtools/intersect/main.nf | 2 +- modules/nf-core/bedtools/makewindows/main.nf | 2 +- modules/nf-core/bedtools/maskfasta/main.nf | 2 +- modules/nf-core/bedtools/merge/main.nf | 2 +- modules/nf-core/bedtools/slop/main.nf | 2 +- modules/nf-core/bedtools/sort/main.nf | 2 +- modules/nf-core/bedtools/split/main.nf | 2 +- modules/nf-core/bedtools/subtract/main.nf | 2 +- modules/nf-core/biobambam/bammerge/main.nf | 2 +- modules/nf-core/biscuit/align/main.nf | 2 +- modules/nf-core/biscuit/biscuitblaster/main.nf | 2 +- modules/nf-core/biscuit/bsconv/main.nf | 2 +- modules/nf-core/biscuit/epiread/main.nf | 2 +- modules/nf-core/biscuit/index/main.nf | 2 +- modules/nf-core/biscuit/mergecg/main.nf | 2 +- modules/nf-core/biscuit/pileup/main.nf | 2 +- modules/nf-core/biscuit/qc/main.nf | 2 +- modules/nf-core/biscuit/vcf2bed/main.nf | 2 +- modules/nf-core/bismark/align/main.nf | 2 +- modules/nf-core/bismark/deduplicate/main.nf | 2 +- modules/nf-core/bismark/genomepreparation/main.nf | 2 +- modules/nf-core/bismark/methylationextractor/main.nf | 2 +- modules/nf-core/bismark/report/main.nf | 2 +- modules/nf-core/bismark/summary/main.nf | 2 +- modules/nf-core/blast/blastn/main.nf | 2 +- modules/nf-core/blast/makeblastdb/main.nf | 2 +- modules/nf-core/blast/tblastn/main.nf | 2 +- modules/nf-core/bowtie/align/main.nf | 2 +- modules/nf-core/bowtie/build/main.nf | 2 +- modules/nf-core/bowtie2/build/main.nf | 2 +- modules/nf-core/bracken/bracken/main.nf | 2 +- modules/nf-core/bracken/combinebrackenoutputs/main.nf | 2 +- modules/nf-core/busco/main.nf | 2 +- modules/nf-core/bwa/aln/main.nf | 2 +- modules/nf-core/bwa/index/main.nf | 2 +- modules/nf-core/bwa/mem/main.nf | 2 +- modules/nf-core/bwa/sampe/main.nf | 2 +- modules/nf-core/bwa/samse/main.nf | 2 +- modules/nf-core/bwamem2/index/main.nf | 2 +- modules/nf-core/bwamem2/mem/main.nf | 2 +- modules/nf-core/bwameth/align/main.nf | 2 +- modules/nf-core/bwameth/index/main.nf | 2 +- modules/nf-core/cat/cat/main.nf | 2 +- modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/centrifuge/centrifuge/main.nf | 2 +- modules/nf-core/centrifuge/kreport/main.nf | 2 +- modules/nf-core/checkm/lineagewf/main.nf | 2 +- modules/nf-core/checkm/qa/main.nf | 2 +- modules/nf-core/chromap/chromap/main.nf | 2 +- modules/nf-core/chromap/index/main.nf | 2 +- modules/nf-core/clonalframeml/main.nf | 2 +- modules/nf-core/cmseq/polymut/main.nf | 2 +- modules/nf-core/cnvkit/antitarget/main.nf | 2 +- modules/nf-core/cnvkit/batch/main.nf | 2 +- modules/nf-core/cnvkit/reference/main.nf | 2 +- modules/nf-core/cnvpytor/callcnvs/main.nf | 2 +- modules/nf-core/cnvpytor/histogram/main.nf | 2 +- modules/nf-core/cnvpytor/importreaddepth/main.nf | 2 +- modules/nf-core/cnvpytor/partition/main.nf | 2 +- modules/nf-core/cnvpytor/view/main.nf | 2 +- modules/nf-core/controlfreec/assesssignificance/main.nf | 2 +- modules/nf-core/controlfreec/freec/main.nf | 2 +- modules/nf-core/controlfreec/freec2bed/main.nf | 2 +- modules/nf-core/controlfreec/freec2circos/main.nf | 2 +- modules/nf-core/controlfreec/makegraph/main.nf | 2 +- modules/nf-core/cooler/cload/main.nf | 2 +- modules/nf-core/cooler/digest/main.nf | 2 +- modules/nf-core/cooler/dump/main.nf | 2 +- modules/nf-core/cooler/merge/main.nf | 2 +- modules/nf-core/cooler/zoomify/main.nf | 2 +- modules/nf-core/crumble/main.nf | 2 +- modules/nf-core/csvtk/concat/main.nf | 2 +- modules/nf-core/csvtk/split/main.nf | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/custom/getchromsizes/main.nf | 2 +- modules/nf-core/custom/sratoolsncbisettings/main.nf | 2 +- modules/nf-core/cutadapt/main.nf | 2 +- modules/nf-core/damageprofiler/main.nf | 2 +- modules/nf-core/dastool/dastool/main.nf | 2 +- modules/nf-core/dastool/fastatocontig2bin/main.nf | 2 +- modules/nf-core/dastool/scaffolds2bin/main.nf | 2 +- modules/nf-core/deeparg/downloaddata/main.nf | 2 +- modules/nf-core/deeparg/predict/main.nf | 2 +- modules/nf-core/deepbgc/download/main.nf | 2 +- modules/nf-core/deepbgc/pipeline/main.nf | 2 +- modules/nf-core/deeptools/bamcoverage/main.nf | 2 +- modules/nf-core/deeptools/computematrix/main.nf | 2 +- modules/nf-core/deeptools/plotfingerprint/main.nf | 2 +- modules/nf-core/deeptools/plotheatmap/main.nf | 2 +- modules/nf-core/deeptools/plotprofile/main.nf | 2 +- modules/nf-core/delly/call/main.nf | 2 +- modules/nf-core/diamond/blastp/main.nf | 2 +- modules/nf-core/diamond/blastx/main.nf | 2 +- modules/nf-core/diamond/makedb/main.nf | 2 +- modules/nf-core/dragmap/align/main.nf | 2 +- modules/nf-core/dragmap/hashtable/main.nf | 2 +- modules/nf-core/dragonflye/main.nf | 2 +- modules/nf-core/dshbio/exportsegments/main.nf | 2 +- modules/nf-core/dshbio/filterbed/main.nf | 2 +- modules/nf-core/dshbio/filtergff3/main.nf | 2 +- modules/nf-core/dshbio/splitbed/main.nf | 2 +- modules/nf-core/dshbio/splitgff3/main.nf | 2 +- modules/nf-core/ectyper/main.nf | 2 +- modules/nf-core/elprep/filter/main.nf | 2 +- modules/nf-core/elprep/merge/main.nf | 2 +- modules/nf-core/elprep/split/main.nf | 2 +- modules/nf-core/emboss/seqret/main.nf | 2 +- modules/nf-core/emmtyper/main.nf | 2 +- modules/nf-core/endorspy/main.nf | 2 +- modules/nf-core/ensemblvep/main.nf | 2 +- modules/nf-core/entrezdirect/esearch/main.nf | 2 +- modules/nf-core/entrezdirect/esummary/main.nf | 2 +- modules/nf-core/entrezdirect/xtract/main.nf | 2 +- modules/nf-core/epang/main.nf | 2 +- modules/nf-core/expansionhunter/main.nf | 2 +- modules/nf-core/faqcs/main.nf | 3 +-- modules/nf-core/fargene/main.nf | 2 +- modules/nf-core/fastani/main.nf | 2 +- modules/nf-core/fastawindows/main.nf | 2 +- modules/nf-core/fastp/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/fastqscan/main.nf | 2 +- modules/nf-core/fasttree/main.nf | 2 +- modules/nf-core/ffq/main.nf | 2 +- modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 2 +- modules/nf-core/fgbio/fastqtobam/main.nf | 2 +- modules/nf-core/fgbio/groupreadsbyumi/main.nf | 2 +- modules/nf-core/fgbio/sortbam/main.nf | 3 +-- modules/nf-core/fgbio/zipperbams/main.nf | 2 +- modules/nf-core/filtlong/main.nf | 2 +- modules/nf-core/flash/main.nf | 2 +- modules/nf-core/flye/main.nf | 2 +- modules/nf-core/freebayes/main.nf | 2 +- modules/nf-core/gamma/gamma/main.nf | 2 +- modules/nf-core/gappa/examineassign/main.nf | 2 +- modules/nf-core/gappa/examinegraft/main.nf | 2 +- modules/nf-core/gappa/examineheattree/main.nf | 2 +- modules/nf-core/gatk/indelrealigner/main.nf | 2 +- modules/nf-core/gatk/realignertargetcreator/main.nf | 2 +- modules/nf-core/gatk/unifiedgenotyper/main.nf | 2 +- modules/nf-core/gatk4/applybqsr/main.nf | 2 +- modules/nf-core/gatk4/applyvqsr/main.nf | 2 +- modules/nf-core/gatk4/baserecalibrator/main.nf | 2 +- modules/nf-core/gatk4/bedtointervallist/main.nf | 2 +- modules/nf-core/gatk4/calculatecontamination/main.nf | 2 +- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 2 +- modules/nf-core/gatk4/collectreadcounts/main.nf | 2 +- modules/nf-core/gatk4/collectsvevidence/main.nf | 2 +- modules/nf-core/gatk4/combinegvcfs/main.nf | 2 +- modules/nf-core/gatk4/composestrtablefile/main.nf | 2 +- modules/nf-core/gatk4/createsequencedictionary/main.nf | 2 +- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 2 +- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 2 +- modules/nf-core/gatk4/fastqtosam/main.nf | 2 +- modules/nf-core/gatk4/filtervarianttranches/main.nf | 2 +- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 2 +- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 2 +- modules/nf-core/gatk4/genomicsdbimport/main.nf | 2 +- modules/nf-core/gatk4/genotypegvcfs/main.nf | 2 +- modules/nf-core/gatk4/getpileupsummaries/main.nf | 2 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 2 +- modules/nf-core/gatk4/indexfeaturefile/main.nf | 2 +- modules/nf-core/gatk4/intervallisttobed/main.nf | 2 +- modules/nf-core/gatk4/intervallisttools/main.nf | 2 +- modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 2 +- modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 2 +- modules/nf-core/gatk4/markduplicates/main.nf | 2 +- modules/nf-core/gatk4/mergebamalignment/main.nf | 2 +- modules/nf-core/gatk4/mergemutectstats/main.nf | 2 +- modules/nf-core/gatk4/mergevcfs/main.nf | 2 +- modules/nf-core/gatk4/mutect2/main.nf | 2 +- modules/nf-core/gatk4/printsvevidence/main.nf | 2 +- modules/nf-core/gatk4/reblockgvcf/main.nf | 2 +- modules/nf-core/gatk4/revertsam/main.nf | 2 +- modules/nf-core/gatk4/samtofastq/main.nf | 2 +- modules/nf-core/gatk4/selectvariants/main.nf | 2 +- modules/nf-core/gatk4/splitintervals/main.nf | 2 +- modules/nf-core/gatk4/splitncigarreads/main.nf | 2 +- modules/nf-core/gatk4/variantfiltration/main.nf | 2 +- modules/nf-core/gatk4/variantrecalibrator/main.nf | 2 +- modules/nf-core/gecco/run/main.nf | 2 +- modules/nf-core/genmap/index/main.nf | 2 +- modules/nf-core/genmap/mappability/main.nf | 2 +- modules/nf-core/genmod/annotate/main.nf | 2 +- modules/nf-core/genmod/compound/main.nf | 2 +- modules/nf-core/genmod/models/main.nf | 2 +- modules/nf-core/genmod/score/main.nf | 2 +- modules/nf-core/genomescope2/main.nf | 2 +- modules/nf-core/genotyphi/parse/main.nf | 2 +- modules/nf-core/genrich/main.nf | 2 +- modules/nf-core/gfaffix/main.nf | 2 +- modules/nf-core/gffread/main.nf | 2 +- modules/nf-core/glimpse/chunk/main.nf | 2 +- 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+- modules/nf-core/md5sum/main.nf | 2 +- modules/nf-core/medaka/main.nf | 2 +- modules/nf-core/megahit/main.nf | 2 +- modules/nf-core/megan/daa2info/main.nf | 2 +- modules/nf-core/megan/rma2info/main.nf | 2 +- modules/nf-core/meningotype/main.nf | 2 +- modules/nf-core/merqury/main.nf | 2 +- modules/nf-core/meryl/count/main.nf | 2 +- modules/nf-core/meryl/histogram/main.nf | 2 +- modules/nf-core/meryl/unionsum/main.nf | 2 +- modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf | 2 +- modules/nf-core/metabat2/metabat2/main.nf | 2 +- modules/nf-core/metaphlan3/mergemetaphlantables/main.nf | 2 +- modules/nf-core/metaphlan3/metaphlan3/main.nf | 2 +- modules/nf-core/methyldackel/extract/main.nf | 2 +- modules/nf-core/methyldackel/mbias/main.nf | 2 +- modules/nf-core/minia/main.nf | 2 +- modules/nf-core/miniasm/main.nf | 2 +- modules/nf-core/minimap2/align/main.nf | 2 +- modules/nf-core/minimap2/index/main.nf | 2 +- modules/nf-core/mlst/main.nf | 2 +- 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modules/nf-core/plasmidid/main.nf | 2 +- modules/nf-core/plink/extract/main.nf | 2 +- modules/nf-core/plink/vcf/main.nf | 2 +- modules/nf-core/plink2/extract/main.nf | 2 +- modules/nf-core/plink2/score/main.nf | 2 +- modules/nf-core/plink2/vcf/main.nf | 2 +- modules/nf-core/pmdtools/filter/main.nf | 2 +- modules/nf-core/porechop/main.nf | 2 +- modules/nf-core/preseq/ccurve/main.nf | 2 +- modules/nf-core/preseq/lcextrap/main.nf | 2 +- modules/nf-core/prinseqplusplus/main.nf | 2 +- modules/nf-core/prodigal/main.nf | 2 +- modules/nf-core/prokka/main.nf | 2 +- modules/nf-core/pycoqc/main.nf | 2 +- modules/nf-core/pydamage/analyze/main.nf | 2 +- modules/nf-core/pydamage/filter/main.nf | 2 +- modules/nf-core/qcat/main.nf | 2 +- modules/nf-core/qualimap/bamqc/main.nf | 2 +- modules/nf-core/qualimap/bamqccram/main.nf | 2 +- modules/nf-core/qualimap/rnaseq/main.nf | 2 +- modules/nf-core/quast/main.nf | 2 +- modules/nf-core/racon/main.nf | 2 +- modules/nf-core/rapidnj/main.nf | 2 +- 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modules/nf-core/samblaster/main.nf | 2 +- modules/nf-core/samtools/ampliconclip/main.nf | 2 +- modules/nf-core/samtools/bam2fq/main.nf | 2 +- modules/nf-core/samtools/collate/main.nf | 2 +- modules/nf-core/samtools/collatefastq/main.nf | 2 +- modules/nf-core/samtools/convert/main.nf | 2 +- modules/nf-core/samtools/depth/main.nf | 2 +- modules/nf-core/samtools/dict/main.nf | 2 +- modules/nf-core/samtools/faidx/main.nf | 2 +- modules/nf-core/samtools/fasta/main.nf | 2 +- modules/nf-core/samtools/fastq/main.nf | 2 +- modules/nf-core/samtools/fixmate/main.nf | 2 +- modules/nf-core/samtools/flagstat/main.nf | 2 +- modules/nf-core/samtools/getrg/main.nf | 2 +- modules/nf-core/samtools/idxstats/main.nf | 2 +- modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/markdup/main.nf | 2 +- modules/nf-core/samtools/merge/main.nf | 2 +- modules/nf-core/samtools/mpileup/main.nf | 2 +- modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/scoary/main.nf | 2 +- modules/nf-core/scramble/clusteranalysis/main.nf | 2 +- modules/nf-core/scramble/clusteridentifier/main.nf | 2 +- modules/nf-core/seacr/callpeak/main.nf | 2 +- modules/nf-core/seqkit/pair/main.nf | 2 +- modules/nf-core/seqkit/replace/main.nf | 2 +- modules/nf-core/seqkit/split2/main.nf | 2 +- modules/nf-core/seqkit/stats/main.nf | 2 +- modules/nf-core/seqsero2/main.nf | 2 +- modules/nf-core/seqtk/mergepe/main.nf | 2 +- modules/nf-core/seqtk/rename/main.nf | 2 +- modules/nf-core/seqtk/sample/main.nf | 2 +- modules/nf-core/seqtk/seq/main.nf | 2 +- modules/nf-core/seqtk/subseq/main.nf | 2 +- modules/nf-core/sequenzautils/bam2seqz/main.nf | 2 +- modules/nf-core/sequenzautils/gcwiggle/main.nf | 2 +- modules/nf-core/seqwish/induce/main.nf | 2 +- modules/nf-core/seroba/run/main.nf | 2 +- modules/nf-core/sexdeterrmine/main.nf | 2 +- modules/nf-core/shasta/main.nf | 2 +- modules/nf-core/shasum/main.nf | 2 +- modules/nf-core/shigatyper/main.nf | 2 +- modules/nf-core/shovill/main.nf | 2 +- modules/nf-core/sistr/main.nf | 2 +- modules/nf-core/slimfastq/main.nf | 2 +- modules/nf-core/snapaligner/align/main.nf | 2 +- modules/nf-core/snapaligner/index/main.nf | 2 +- modules/nf-core/snippy/core/main.nf | 2 +- modules/nf-core/snippy/run/main.nf | 2 +- modules/nf-core/snpdists/main.nf | 2 +- modules/nf-core/snpeff/main.nf | 2 +- modules/nf-core/snpsift/split/main.nf | 2 +- modules/nf-core/snpsites/main.nf | 2 +- modules/nf-core/somalier/extract/main.nf | 2 +- modules/nf-core/somalier/relate/main.nf | 2 +- modules/nf-core/sortmerna/main.nf | 2 +- modules/nf-core/sourmash/sketch/main.nf | 2 +- modules/nf-core/spades/main.nf | 2 +- modules/nf-core/spatyper/main.nf | 2 +- modules/nf-core/sratools/fasterqdump/main.nf | 2 +- modules/nf-core/sratools/prefetch/main.nf | 2 +- modules/nf-core/srst2/srst2/main.nf | 2 +- modules/nf-core/ssuissero/main.nf | 2 +- modules/nf-core/stadeniolib/scramble/main.nf | 2 +- modules/nf-core/staphopiasccmec/main.nf | 2 +- modules/nf-core/star/align/main.nf | 2 +- modules/nf-core/star/genomegenerate/main.nf | 2 +- modules/nf-core/stranger/main.nf | 2 +- modules/nf-core/strelka/germline/main.nf | 2 +- modules/nf-core/strelka/somatic/main.nf | 2 +- modules/nf-core/stringtie/merge/main.nf | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 2 +- modules/nf-core/subread/featurecounts/main.nf | 2 +- modules/nf-core/svdb/merge/main.nf | 2 +- modules/nf-core/svdb/query/main.nf | 2 +- modules/nf-core/svtk/standardize/main.nf | 2 +- modules/nf-core/tabix/bgziptabix/main.nf | 2 +- modules/nf-core/tabix/tabix/main.nf | 2 +- modules/nf-core/tailfindr/main.nf | 2 +- modules/nf-core/tbprofiler/profile/main.nf | 2 +- modules/nf-core/tiddit/cov/main.nf | 2 +- modules/nf-core/tiddit/sv/main.nf | 2 +- modules/nf-core/transdecoder/longorf/main.nf | 2 +- modules/nf-core/transdecoder/predict/main.nf | 2 +- modules/nf-core/trimgalore/main.nf | 2 +- modules/nf-core/trimmomatic/main.nf | 2 +- modules/nf-core/ucsc/bedclip/main.nf | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 2 +- modules/nf-core/ucsc/bedtobigbed/main.nf | 2 +- modules/nf-core/ucsc/bigwigaverageoverbed/main.nf | 2 +- modules/nf-core/ucsc/liftover/main.nf | 2 +- modules/nf-core/ucsc/wigtobigwig/main.nf | 2 +- modules/nf-core/ultra/align/main.nf | 2 +- modules/nf-core/ultra/index/main.nf | 2 +- modules/nf-core/ultra/pipeline/main.nf | 2 +- modules/nf-core/umitools/dedup/main.nf | 2 +- modules/nf-core/umitools/extract/main.nf | 2 +- modules/nf-core/unicycler/main.nf | 2 +- modules/nf-core/untar/main.nf | 2 +- modules/nf-core/unzip/main.nf | 2 +- modules/nf-core/vardictjava/main.nf | 2 +- modules/nf-core/variantbam/main.nf | 2 +- modules/nf-core/vcf2db/main.nf | 2 +- modules/nf-core/vcf2maf/main.nf | 2 +- modules/nf-core/vcfanno/main.nf | 2 +- modules/nf-core/vcflib/vcfbreakmulti/main.nf | 2 +- modules/nf-core/vcflib/vcfuniq/main.nf | 2 +- modules/nf-core/vcftools/main.nf | 2 +- modules/nf-core/verifybamid/verifybamid2/main.nf | 2 +- modules/nf-core/vsearch/sintax/main.nf | 2 +- modules/nf-core/vsearch/usearchglobal/main.nf | 2 +- modules/nf-core/wgsim/main.nf | 2 +- modules/nf-core/whamg/main.nf | 2 +- modules/nf-core/yara/index/main.nf | 2 +- modules/nf-core/yara/mapper/main.nf | 2 +- tests/modules/nf-core/vcf2maf/nextflow.config | 2 +- 610 files changed, 610 insertions(+), 612 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index d99ba63cdf8..5e0f28f98e1 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -4,7 +4,7 @@ process ABACAS { conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) def container_image = "/abacas:1.3.1--pl526_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index 9dae4716625..feb389602ed 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -4,7 +4,7 @@ process ABRICATE_RUN { conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) def container_image = "/abricate%3A1.0.1--ha8f3691_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index a618ffe9f49..c1e1c5f634b 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -4,7 +4,7 @@ process ABRICATE_SUMMARY { conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) def container_image = "/abricate%3A1.0.1--ha8f3691_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 2119f98be10..692beeb33af 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -4,7 +4,7 @@ process ADAPTERREMOVAL { conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) def container_image = "/adapterremoval:2.3.2--hb7ba0dd_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 50f4fe8d0bf..373622dc139 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -5,7 +5,7 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) def container_image = "/adapterremovalfixprefix:0.0.5--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index d49d010bff4..39f5b1c3615 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -4,7 +4,7 @@ process AGRVATE { conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) def container_image = "/agrvate:1.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index 0a9ea5dc3ba..4f85ae6ad68 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -4,7 +4,7 @@ process ALLELECOUNTER { conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) def container_image = "/cancerit-allelecount:4.3.0--h41abebc_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index a038bce4ecf..b9641759dd5 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -4,7 +4,7 @@ process AMPIR { conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) def container_image = "/r-ampir:1.1.0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index c42ef6b172d..8a11242273d 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -5,7 +5,7 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) def container_image = "/amplify:1.0.3--py36hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 6b084fc3ace..a50b4eb9464 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -3,7 +3,7 @@ process AMPS { conda (params.enable_conda ? "bioconda::hops=0.35" : null) def container_image = "/hops:0.35--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 63f5b0b0a0a..8180999ee80 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -4,7 +4,7 @@ process AMRFINDERPLUS_RUN { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 27456eee12d..e60ee7d62a3 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -4,7 +4,7 @@ process AMRFINDERPLUS_UPDATE { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n output: diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index 66028a9058d..bfe1bdef1cc 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -4,7 +4,7 @@ process ANGSD_DOCOUNTS { conda (params.enable_conda ? "bioconda::angsd=0.939" : null) def container_image = "/angsd:0.939--h468462d_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 2859d6005d0..8f6f157c447 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -4,7 +4,7 @@ process ANTISMASH_ANTISMASHLITE { conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } containerOptions { "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index d2e5c66b89a..c62d9e0e4ad 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -3,7 +3,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 41455f42199..55f10f6cf8f 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -5,7 +5,7 @@ process ARIA2 { conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) def container_image = "/aria2:1.36.0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index ab1f9d50af8..4ba19dd2fc0 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -4,7 +4,7 @@ process ARIBA_GETREF { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) def container_image = "/ariba:2.14.6--py39h67e14b5_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 3060c8e6bad..351daa2e950 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -4,7 +4,7 @@ process ARIBA_RUN { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) def container_image = "/ariba:2.14.6--py39h67e14b5_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index d826303d295..7cf484e057c 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -4,7 +4,7 @@ process ARRIBA { conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) def container_image = "/arriba:2.3.0--haa8aa89_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 410fba484c6..76f94bf78a7 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -4,7 +4,7 @@ process ARTIC_GUPPYPLEX { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) def container_image = "/artic:1.2.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index cad99f79409..fd9d38f54d1 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -4,7 +4,7 @@ process ARTIC_MINION { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) def container_image = "/artic:1.2.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index 973f286d40e..3dcb3240176 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -4,7 +4,7 @@ process ASCAT { conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) def container_image = "/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 23baf502ee2..2e04c149f45 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -4,7 +4,7 @@ process ASSEMBLYSCAN { conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) def container_image = "/assembly-scan:0.4.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index 55ae0be671b..df5dd589db2 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -4,7 +4,7 @@ process ATAQV_ATAQV { conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) def container_image = "/ataqv:1.3.0--py39hccc85d7_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(peak_file) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 4b9ef598bf0..a45a63f76db 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -3,7 +3,7 @@ process ATAQV_MKARV { conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) def container_image = "/ataqv:1.3.0--py39hccc85d7_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 05a53341b99..b278fe0c8fa 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -4,7 +4,7 @@ process ATLAS_CALL { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index cbbba2b4733..1d2f542800e 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -4,7 +4,7 @@ process ATLAS_PMD { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index e5d42fbcbca..e487b5a5e99 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -4,7 +4,7 @@ process ATLAS_RECAL { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index 8ebe9785a38..e6a93a1c436 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -4,7 +4,7 @@ process ATLAS_SPLITMERGE { conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index c29f6548727..a2f36f22304 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -4,7 +4,7 @@ process BAKTA { conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) def container_image = "/bakta:1.5.0--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index 154444f207c..f5039580cd9 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -4,7 +4,7 @@ process BAMALIGNCLEANER { conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) def container_image = "/bamaligncleaner:0.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 3b8863800cf..e6bae7ffaea 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -4,7 +4,7 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) def container_image = "/bamcmp:2.2--h05f6578_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index c8c3b561538..7fb6588e0d1 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -4,7 +4,7 @@ process BAMTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) def container_image = "/bamtools:2.5.1--h9a82719_9" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index ca3cdfb3bdb..cd4120d5b52 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -4,7 +4,7 @@ process BAMTOOLS_SPLIT { conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) def container_image = "/bamtools:2.5.2--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index 4d82b8f50ae..a686f37c8f7 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -4,7 +4,7 @@ process BAMTOOLS_STATS { conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) def container_image = "/bamtools:2.5.1--h9a82719_9" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 13e72741cd8..767b821510d 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -4,7 +4,7 @@ process BAMUTIL_TRIMBAM { conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) def container_image = "/bamutil:1.0.15--h2e03b76_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 3550e57b711..173f8dd8298 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -4,7 +4,7 @@ process BANDAGE_IMAGE { conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) def container_image = "/bandage:0.8.1--hc9558a2_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 9adb38b4405..8bf12c5975f 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -4,7 +4,7 @@ process BBMAP_ALIGN { conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index b10ff1a0999..a9be0864f8b 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -4,7 +4,7 @@ process BBMAP_BBDUK { conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) def container_image = "/bbmap:38.90--he522d1c_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 82ecb35cdad..287de1fffce 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -3,7 +3,7 @@ process BBMAP_BBSPLIT { conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) def container_image = "/bbmap:38.93--he522d1c_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index 8563a1f8cf9..8183ff129d4 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -5,7 +5,7 @@ process BBMAP_CLUMPIFY { conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) def container_image = "/bbmap:38.98--h5c4e2a8_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index 1fdf2a7e3a0..9887f0add27 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -4,7 +4,7 @@ process BBMAP_INDEX { conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) def container_image = "/bbmap:38.92--he522d1c_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index de6bfede58b..15504d3f7d7 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -4,7 +4,7 @@ process BBMAP_PILEUP { conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 7a501948c4b..8ef222462a0 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_ANNOTATE { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 5526bc95107..934ba4640e2 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_CONCAT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index 4da9c561106..f8939b6775f 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_CONSENSUS { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index 35eb9b3472d..2d9034a3824 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index e83316082e5..7deb4c91a03 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_FILTER { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 5ff7c80a1ee..3c49d6c5e68 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_INDEX { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 9b7ce499ee1..27832fd30f8 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_ISEC { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 27429cac3e3..91931601a07 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_MERGE { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index 816dc7faa30..b41b3e349ff 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_MPILEUP { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 87853ecabf0..a1754c6097d 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_NORM { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 70c89d7377f..826eed5cdff 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_QUERY { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index da4b1472434..3a996aa0b27 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_REHEADER { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 41b9711f635..d09ede97182 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_ROH { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 436d1c194c2..926a4e1f314 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_SORT { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 0792b6ac95e..e9569da3cbe 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_STATS { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 7602dac552e..3e7b8e2786c 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -4,7 +4,7 @@ process BCFTOOLS_VIEW { conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index 9df47150549..63b0b7a29e5 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_BAMTOBED { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index c3b2e5bd307..70cfced86f3 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_COMPLEMENT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index aa7643c189b..a1c15efed49 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_GENOMECOV { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 848fa5373c2..263b1d9de27 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_GETFASTA { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path bed diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index cc0a4eb8d29..a6fc8f7d54e 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_INTERSECT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index f74e8e8a906..30b76025828 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_MAKEWINDOWS { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--h7d7f7ad_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(regions) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index 51b1caa7f23..7f4b4a7556e 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_MASKFASTA { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index b50b5a30c4c..2ab5f472b07 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_MERGE { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index 51ec0f2f685..d538e87bb82 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_SLOP { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 17dc46cc08e..2376227ca93 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_SORT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index 23ea1eade81..9d116139d34 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_SPLIT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--h468198e_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index dcc86ed01bd..0cb02fd110f 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_SUBTRACT { conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index cc3f60782db..13e7b17efbb 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -4,7 +4,7 @@ process BIOBAMBAM_BAMMERGE { conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) def container_image = "/biobambam:2.0.183--h9f5acd7_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index 3a012037a57..95aa4fa06cf 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -4,7 +4,7 @@ process BISCUIT_ALIGN { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 757064ecd2e..bc9b6992ff1 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -4,7 +4,7 @@ process BISCUIT_BLASTER { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index 6903d42f0f9..290fae18774 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -4,7 +4,7 @@ process BISCUIT_BSCONV { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index c21e1d347ed..06780e35cfa 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -4,7 +4,7 @@ process BISCUIT_EPIREAD { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(snp_bed) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 7d982439859..b5cf5917efa 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -4,7 +4,7 @@ process BISCUIT_INDEX { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index 7d5935dfe26..eb7e2175654 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -4,7 +4,7 @@ process BISCUIT_MERGECG { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index b683ed7d414..15839eb00ab 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -4,7 +4,7 @@ process BISCUIT_PILEUP { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index 220cb8ae934..efbe6afaa57 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -4,7 +4,7 @@ process BISCUIT_QC { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 3bae4d43a09..26d5570bfcd 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -4,7 +4,7 @@ process BISCUIT_VCF2BED { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index 54401f610db..6922160ed5d 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -4,7 +4,7 @@ process BISMARK_ALIGN { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index b5b211276aa..b3dc6d9a502 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -4,7 +4,7 @@ process BISMARK_DEDUPLICATE { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 56e7a1bbc0c..85619f385f3 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -4,7 +4,7 @@ process BISMARK_GENOMEPREPARATION { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index a265c913a2d..1012bd2ed27 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -4,7 +4,7 @@ process BISMARK_METHYLATIONEXTRACTOR { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 5933747a724..80307f9531d 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -4,7 +4,7 @@ process BISMARK_REPORT { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 52e4fb4e502..a760dc4f3f8 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -3,7 +3,7 @@ process BISMARK_SUMMARY { conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path(bam) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index c4646bf8bec..b4f5e5eb22f 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -4,7 +4,7 @@ process BLAST_BLASTN { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) def container_image = "/blast:2.12.0--pl5262h3289130_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 208fe8c3f86..0f7f3a86b9f 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -4,7 +4,7 @@ process BLAST_MAKEBLASTDB { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) def container_image = "/blast:2.12.0--pl5262h3289130_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 9e2f5c49b9d..9e4afb475ff 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -4,7 +4,7 @@ process BLAST_TBLASTN { conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) def container_image = "/blast:2.12.0--pl5262h3289130_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 513b8f0eff6..af0ccc20463 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,7 +3,7 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) -def container_image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" + def container_image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) input: diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 4eb3ea8ecbf..4ae0d635adc 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -4,7 +4,7 @@ process BOWTIE_BUILD { conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) def container_image = "/bowtie:1.3.0--py38hed8969a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 2a3b2dbf39e..8d28546d4c2 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -4,7 +4,7 @@ process BOWTIE2_BUILD { conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) def container_image = "/bowtie2:2.4.4--py39hbb4e92a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index 5912d7d8c96..aaa70a7c538 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -6,7 +6,7 @@ process BRACKEN_BRACKEN { // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) def container_image = "/bracken:2.7--py39hc16433a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(kraken_report) diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 86855e645db..f289c11a309 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -3,7 +3,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { conda (params.enable_conda ? "bioconda::bracken=2.7" : null) def container_image = "/bracken:2.7--py39hc16433a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 162b8199d5d..35a1927b548 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -4,7 +4,7 @@ process BUSCO { conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) def container_image = "/busco:5.4.3--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index f3fd23895b0..446606ebf18 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -4,7 +4,7 @@ process BWA_ALN { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) def container_image = "/bwa:0.7.17--h5bf99c6_8" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index fc1c08302fd..bd7a00e6901 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -4,7 +4,7 @@ process BWA_INDEX { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) def container_image = "/bwa:0.7.17--hed695b0_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 15e138ca15e..c82a8000df2 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -4,7 +4,7 @@ process BWA_MEM { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 3480cba9cdf..690e5e7d748 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -4,7 +4,7 @@ process BWA_SAMPE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 224a686b0c0..3a3f6f455d4 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -4,7 +4,7 @@ process BWA_SAMSE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index d61c1ef6bf8..0e60cf630e6 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -4,7 +4,7 @@ process BWAMEM2_INDEX { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) def container_image = "/bwa-mem2:2.2.1--he513fc3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 93f13141ca8..f61f28d86e4 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -4,7 +4,7 @@ process BWAMEM2_MEM { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 0cc44590b01..df4a7a948ff 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -4,7 +4,7 @@ process BWAMETH_ALIGN { conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) def container_image = "/bwameth:0.2.2--py_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 954b7f06da5..bfff95518cc 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -4,7 +4,7 @@ process BWAMETH_INDEX { conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) def container_image = "/bwameth:0.2.2--py_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 13abc0293c7..a302cfb21d4 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -4,7 +4,7 @@ process CAT_CAT { conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) def container_image = "/pigz:2.3.4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 2ea69fef0cd..113dca719df 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -4,7 +4,7 @@ process CAT_FASTQ { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 467dc07bfc0..c3bda72b511 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -4,7 +4,7 @@ process CENTRIFUGE_CENTRIFUGE { conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index a9dc06d3f31..eef2696eb72 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -4,7 +4,7 @@ process CENTRIFUGE_KREPORT { conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index 82273e4dca0..675c04203f2 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -4,7 +4,7 @@ process CHECKM_LINEAGEWF { conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 079eb5cbb7e..7bf71a35a3c 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -4,7 +4,7 @@ process CHECKM_QA { conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index 839b76806fd..721b3c5333b 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -4,7 +4,7 @@ process CHROMAP_CHROMAP { conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 9ba87bca3e6..a56afc3ec8f 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -4,7 +4,7 @@ process CHROMAP_INDEX { conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) def container_image = "/chromap:0.2.1--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 1209b3e7371..22e207008c4 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -4,7 +4,7 @@ process CLONALFRAMEML { conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) def container_image = "/clonalframeml:1.12--h7d875b9_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index f0d92780e2a..c07276534f2 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -5,7 +5,7 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) def container_image = "/cmseq:1.0.4--pyhb7b1952_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index b5f95e70cf0..521143e0f37 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -4,7 +4,7 @@ process CNVKIT_ANTITARGET { conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 43e05371f1e..fa6a30ed9b2 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -4,7 +4,7 @@ process CNVKIT_BATCH { conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) def container_image = "/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 34020c34615..bc727cebc01 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -4,7 +4,7 @@ process CNVKIT_REFERENCE { conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index 73a8f884c2b..74e5e8332b4 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -4,7 +4,7 @@ process CNVPYTOR_CALLCNVS { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 3b5fbc68dac..609fbe8a9a0 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -4,7 +4,7 @@ process CNVPYTOR_HISTOGRAM { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index 1164c322918..3899e065cb8 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -4,7 +4,7 @@ process CNVPYTOR_IMPORTREADDEPTH { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_file), path(index) diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index fbcbab4acf3..fbb699192b9 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -4,7 +4,7 @@ process CNVPYTOR_PARTITION { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index c3e08baed17..77fd85cfa8d 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -4,7 +4,7 @@ process CNVPYTOR_VIEW { conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pytor_files) diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index dae09d80d61..c7f21fdf527 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -4,7 +4,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 133db341df9..342983de63c 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -4,7 +4,7 @@ process CONTROLFREEC_FREEC { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index e2c6814b4fa..ab6218f9d37 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -4,7 +4,7 @@ process CONTROLFREEC_FREEC2BED { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 959cdcb8d1e..951115daa51 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -4,7 +4,7 @@ process CONTROLFREEC_FREEC2CIRCOS { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index ccd9610a5ef..be4d359a1af 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -4,7 +4,7 @@ process CONTROLFREEC_MAKEGRAPH { conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index d8a424104ce..51d7b7a0727 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -4,7 +4,7 @@ process COOLER_CLOAD { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pairs), path(index) diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index 7b46ca4c5c2..7c4e30ce820 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -4,7 +4,7 @@ process COOLER_DIGEST { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index 2ca1788320d..0bdeef9bdf6 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -4,7 +4,7 @@ process COOLER_DUMP { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index 64daf1fb189..1018657a78a 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -4,7 +4,7 @@ process COOLER_MERGE { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index ac96ec348ff..c5a19fed4cb 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -4,7 +4,7 @@ process COOLER_ZOOMIFY { conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index 762b23ab0c7..b0481e9b1a8 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -4,7 +4,7 @@ process CRUMBLE { conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) def container_image = "/crumble:0.9.0--hb0d9459_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index e5b0a7d2853..02c49d2d820 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -4,7 +4,7 @@ process CSVTK_CONCAT { conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) def container_image = "/csvtk:0.23.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 2004106b7f5..15e3f27b9a7 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -4,7 +4,7 @@ process CSVTK_SPLIT { conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) def container_image = "/csvtk:0.23.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 6d82d817d0b..7ea35504ce8 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,7 +4,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) def container_image = "/multiqc:1.13--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index a57f9ad5016..72950bc8f66 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -4,7 +4,7 @@ process CUSTOM_GETCHROMSIZES { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 74392792ffe..508f303e24c 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -4,7 +4,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path('*.mkfg') , emit: ncbi_settings diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 274a6971311..8643ceb5f73 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -4,7 +4,7 @@ process CUTADAPT { conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) def container_image = "/cutadapt:3.4--py39h38f01e4_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index dfbea26270c..4ccc68c0d60 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -4,7 +4,7 @@ process DAMAGEPROFILER { conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) def container_image = "/damageprofiler:1.1--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index 693caca5e10..721fe5d304a 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -4,7 +4,7 @@ process DASTOOL_DASTOOL { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) def container_image = "/das_tool:1.1.4--r41hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index add35400739..7e8f32092fa 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -4,7 +4,7 @@ process DASTOOL_FASTATOCONTIG2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) def container_image = "/das_tool:1.1.4--r41hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 0b3cd5735e2..bf218d16416 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -4,7 +4,7 @@ process DASTOOL_SCAFFOLDS2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) def container_image = "/das_tool:1.1.3--r41hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index 46b2d9262f5..d51861acb53 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -3,7 +3,7 @@ process DEEPARG_DOWNLOADDATA { conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) def container_image = "/deeparg:1.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 236858986ce..3bef899fe4e 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -4,7 +4,7 @@ process DEEPARG_PREDICT { conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) def container_image = "/deeparg:1.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 99491ff255b..7a07b7c6f01 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -3,7 +3,7 @@ process DEEPBGC_DOWNLOAD { conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index d28d630a4ad..f07619125ef 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -4,7 +4,7 @@ process DEEPBGC_PIPELINE { conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 974b2c16529..48e73850af7 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -4,7 +4,7 @@ process DEEPTOOLS_BAMCOVERAGE { conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index c2a259a17f0..e98e69fc4c0 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -4,7 +4,7 @@ process DEEPTOOLS_COMPUTEMATRIX { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index ee7a7bd4078..8985e3c8dda 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -4,7 +4,7 @@ process DEEPTOOLS_PLOTFINGERPRINT { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index ebd435c2350..bdf1c6c7bb3 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -4,7 +4,7 @@ process DEEPTOOLS_PLOTHEATMAP { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index c2054fb870a..14c1c332805 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -4,7 +4,7 @@ process DEEPTOOLS_PLOTPROFILE { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index 6069c353482..972165afc43 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -4,7 +4,7 @@ process DELLY_CALL { conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) def container_image = "/delly:1.1.5--h358d541_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(exclude_bed) diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index 33c2bf0612e..b8cdadcf157 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -4,7 +4,7 @@ process DIAMOND_BLASTP { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) def container_image = "/diamond:2.0.15--hb97b32f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index e25fb93a31c..3fe5ef002f0 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -4,7 +4,7 @@ process DIAMOND_BLASTX { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) def container_image = "/diamond:2.0.15--hb97b32f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index f7f3d1bd5e8..33764cc226a 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -4,7 +4,7 @@ process DIAMOND_MAKEDB { conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) def container_image = "/diamond:2.0.15--hb97b32f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index d80599b0cd7..7d66c0fe322 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -4,7 +4,7 @@ process DRAGMAP_ALIGN { conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) def container_image = "/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 737c5c9237b..7f2b88bc476 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -4,7 +4,7 @@ process DRAGMAP_HASHTABLE { conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) def container_image = "/dragmap:1.2.1--hd4ca14e_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index 860c932af7c..6ac9142081e 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -4,7 +4,7 @@ process DRAGONFLYE { conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) def container_image = "/dragonflye:1.0.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index f4869027b00..23c36bd5460 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -4,7 +4,7 @@ process DSHBIO_EXPORTSEGMENTS { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 674372c84ac..526f1cfea6e 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -4,7 +4,7 @@ process DSHBIO_FILTERBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index 4990698ec1a..ba2cfe102c4 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -4,7 +4,7 @@ process DSHBIO_FILTERGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index e7e27ff7b33..bd3d319cd02 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -4,7 +4,7 @@ process DSHBIO_SPLITBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 4fc93947e46..619ab53e175 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -4,7 +4,7 @@ process DSHBIO_SPLITGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index ba4a38c3d74..f3cee14d68f 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -4,7 +4,7 @@ process ECTYPER { conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) def container_image = "/ectyper:1.0.0--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 0604c9b131b..1865efd5e57 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -4,7 +4,7 @@ process ELPREP_FILTER { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) def container_image = "/elprep:5.1.2--he881be0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index c403ac880c7..286610269d7 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -4,7 +4,7 @@ process ELPREP_MERGE { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) def container_image = "/elprep:5.1.2--he881be0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 8ba666759e3..0578226659b 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -4,7 +4,7 @@ process ELPREP_SPLIT { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) def container_image = "/elprep:5.1.2--he881be0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 3a752c96580..1d3ff7e8770 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -4,7 +4,7 @@ process EMBOSS_SEQRET { conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) def container_image = "/emboss:6.6.0--hf657eab_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 5974c362580..37d9c30b2e8 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -4,7 +4,7 @@ process EMMTYPER { conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) def container_image = "/emmtyper:0.2.0--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 245305faad6..b3340c7e0b3 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -4,7 +4,7 @@ process ENDORSPY { conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) def container_image = "/endorspy:0.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index 47737aa9688..e5154508187 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -4,7 +4,7 @@ process ENSEMBLVEP { conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) def container_image = "/ensembl-vep:106.1--pl5321h4a94de4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 77574bdd286..855ba93627e 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -4,7 +4,7 @@ process ENTREZDIRECT_ESEARCH { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) def container_image = "/entrez-direct:16.2--he881be0_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(term) diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index 25f79c0e0fe..ec433eee81b 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -4,7 +4,7 @@ process ENTREZDIRECT_ESUMMARY { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) def container_image = "/entrez-direct:16.2--he881be0_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(uid), path(uids_file) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index 144de51f913..d83daadef91 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -4,7 +4,7 @@ process ENTREZDIRECT_XTRACT { conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) def container_image = "/entrez-direct:16.2--he881be0_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(xml_input) diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index 165ed3f2b4c..9656a7e41ef 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -4,7 +4,7 @@ process EPANG { conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) def container_image = "/epa-ng:0.3.8--h9a82719_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(queryaln) diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index ba517b556ce..bbf15a03a3c 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -4,7 +4,7 @@ process EXPANSIONHUNTER { conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) def container_image = "/expansionhunter:4.0.2--he785bd8_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index ae51019e658..472792c1592 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -4,7 +4,7 @@ process FAQCS { conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) def container_image = "/faqcs%3A2.10--r41h9a82719_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) @@ -100,4 +100,3 @@ process FAQCS { """ } } - diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index b3bbb6987e5..c2f43bd2fae 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -5,7 +5,7 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) def container_image = "/fargene:0.1--py27h21c881e_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index 5928d85cea1..4ad24730a57 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -4,7 +4,7 @@ process FASTANI { conda (params.enable_conda ? "bioconda::fastani=1.32" : null) def container_image = "/fastani:1.32--he1c1bb9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query) diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index 6e84dd4c1c8..24c9f42cbce 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -4,7 +4,7 @@ process FASTAWINDOWS { conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) def container_image = "/fasta_windows:0.2.4--hec16e2b_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 823fb5fa547..fb1b5d0f862 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -4,7 +4,7 @@ process FASTP { conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) def container_image = "/fastp:0.23.2--h79da9fb_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 698e0aa48ce..f1db0764e8d 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -4,7 +4,7 @@ process FASTQC { conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) def container_image = "/fastqc:0.11.9--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index a6945e7c8f4..6cbfe9dc52f 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -4,7 +4,7 @@ process FASTQSCAN { conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) def container_image = "/fastq-scan:0.4.4--h7d875b9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 695bd1e1fed..a6aab2f1823 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -3,7 +3,7 @@ process FASTTREE { conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) def container_image = "/fasttree:2.1.10--h516909a_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 7979417787a..9a2a648aca9 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -4,7 +4,7 @@ process FFQ { conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) def container_image = "/ffq:0.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 65f00822fe1..21a8608d811 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -4,7 +4,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index df90958ce3c..84044c635d1 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -4,7 +4,7 @@ process FGBIO_FASTQTOBAM { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 06b3194e747..5e8d651aff2 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -4,7 +4,7 @@ process FGBIO_GROUPREADSBYUMI { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(taggedbam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index bd3c4bb535a..1acfbc9435f 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -4,7 +4,7 @@ process FGBIO_SORTBAM { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) @@ -32,4 +32,3 @@ process FGBIO_SORTBAM { END_VERSIONS """ } - diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 434c8a3c36b..6b6839ed607 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -4,7 +4,7 @@ process FGBIO_ZIPPERBAMS { conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(unmapped_bam) diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index a331ded8cc0..7f23797415f 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -4,7 +4,7 @@ process FILTLONG { conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) def container_image = "/filtlong:0.2.1--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index c2b5ac9b82e..f743ea592be 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -3,7 +3,7 @@ process FLASH { label 'process_medium' def container_image = "/flash:1.2.11--hed695b0_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 2ad053cd465..c1e177ef033 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -4,7 +4,7 @@ process FLYE { conda (params.enable_conda ? "bioconda::flye=2.9" : null) def container_image = "/flye:2.9--py39h6935b12_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index db9e79a18b5..4fda2889ec8 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -4,7 +4,7 @@ process FREEBAYES { conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) def container_image = "/freebayes:1.3.5--py38ha193a2f_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index e184b2bd9de..0f759462f23 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -6,7 +6,7 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) def container_image = "/gamma%3A2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 1bd28feb658..744c2b80b1b 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -4,7 +4,7 @@ process GAPPA_EXAMINEASSIGN { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) def container_image = "/gappa:0.8.0--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 013854da8f4..2540110305c 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -4,7 +4,7 @@ process GAPPA_EXAMINEGRAFT { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) def container_image = "/gappa:0.8.0--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 47540550260..c4ac834e28d 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -4,7 +4,7 @@ process GAPPA_EXAMINEHEATTREE { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) def container_image = "/gappa:0.8.0--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 721a81beb3c..e6ae6fd0336 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -4,7 +4,7 @@ process GATK_INDELREALIGNER { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) def container_image = "/gatk:3.5--hdfd78af_11" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index 93673eee6f2..bae7d15c9dc 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -4,7 +4,7 @@ process GATK_REALIGNERTARGETCREATOR { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) def container_image = "/gatk:3.5--hdfd78af_11" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index d314ae4bf34..2c74974bac4 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -4,7 +4,7 @@ process GATK_UNIFIEDGENOTYPER { conda (params.enable_conda ? "bioconda::gatk=3.5" : null) def container_image = "/gatk:3.5--hdfd78af_11" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 5c98a3bf652..cf49c523ac0 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,7 +4,7 @@ process GATK4_APPLYBQSR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 82c197e16c2..f7f645824f1 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -4,7 +4,7 @@ process GATK4_APPLYVQSR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 20c669fc144..1451b91ef45 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,7 +4,7 @@ process GATK4_BASERECALIBRATOR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 8b21e323a78..3482798a59b 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,7 +4,7 @@ process GATK4_BEDTOINTERVALLIST { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index f20566296e1..4a21a9633c9 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,7 +4,7 @@ process GATK4_CALCULATECONTAMINATION { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 6035de8121e..aaede205c5d 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,7 +4,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 96d2e167b01..aa99564a5df 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -4,7 +4,7 @@ process GATK4_COLLECTREADCOUNTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 2e67748b856..4872e413164 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -4,7 +4,7 @@ process GATK4_COLLECTSVEVIDENCE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 370c6b256f9..9bbe4cbc94e 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,7 +4,7 @@ process GATK4_COMBINEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 6a6f7851972..12c74e8fc90 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,7 +4,7 @@ process GATK4_COMPOSESTRTABLEFILE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index ab99054765f..5fc913eccca 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,7 +4,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index e3b3738c29a..bdb2b490668 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -4,7 +4,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 39ae064093f..de7a9129798 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -4,7 +4,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 8cc3c638c58..16f18ba5f21 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -4,7 +4,7 @@ process GATK4_FASTQTOSAM { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 31ef85c4d06..7747bf521b7 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,7 +4,7 @@ process GATK4_FILTERVARIANTTRANCHES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index c271e5e191d..edc9593532d 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -4,7 +4,7 @@ process GATK4_GATHERBQSRREPORTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index b4a69bd5b11..a2c9221aaba 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,7 +4,7 @@ process GATK4_GATHERPILEUPSUMMARIES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 4a840ed5b9f..16c9275e778 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,7 +4,7 @@ process GATK4_GENOMICSDBIMPORT { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 863858417fd..7966cf5d391 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,7 +4,7 @@ process GATK4_GENOTYPEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 9a11fb4ee9c..55654ce8cdc 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,7 +4,7 @@ process GATK4_GETPILEUPSUMMARIES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 83fe3296c26..216214089f0 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,7 +4,7 @@ process GATK4_HAPLOTYPECALLER { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 32924ff2cef..50658a9d1ab 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,7 +4,7 @@ process GATK4_INDEXFEATUREFILE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 3354ce12618..1871cf32cb9 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,7 +4,7 @@ process GATK4_INTERVALLISTTOBED { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 8fb194ec1e6..c2738d5fbef 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,7 +4,7 @@ process GATK4_INTERVALLISTTOOLS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 9daf8cbf429..f7ae47d5af3 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,7 +4,7 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index cde0ec474e0..5e398e9c1cc 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -4,7 +4,7 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 334b971e5e5..a95df5d13a7 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -4,7 +4,7 @@ process GATK4_MARKDUPLICATES { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 8d1986b7aa6..34072eccfee 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -4,7 +4,7 @@ process GATK4_MERGEBAMALIGNMENT { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 758a0c41439..5391b9b20d5 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,7 +4,7 @@ process GATK4_MERGEMUTECTSTATS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index a0b67fcba63..7874740ff43 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -4,7 +4,7 @@ process GATK4_MERGEVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 7ba9cedcf69..ebfcd88afcd 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -4,7 +4,7 @@ process GATK4_MUTECT2 { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index d744988dbff..4c479a66a04 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -4,7 +4,7 @@ process GATK4_PRINTSVEVIDENCE { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 75ec7370a73..8faa33a416a 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -4,7 +4,7 @@ process GATK4_REBLOCKGVCF { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 7a61d91b5ce..9f12b3998fc 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -4,7 +4,7 @@ process GATK4_REVERTSAM { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 89111d57f3e..3ca36df61fc 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -4,7 +4,7 @@ process GATK4_SAMTOFASTQ { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 018e633b387..09147f2da2c 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -4,7 +4,7 @@ process GATK4_SELECTVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index b50b8fa18ab..1985cf3f107 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -4,7 +4,7 @@ process GATK4_SPLITINTERVALS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 8ace4b68e56..74cf1d54cf3 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -4,7 +4,7 @@ process GATK4_SPLITNCIGARREADS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index cbafd73df92..ac39d31540c 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -4,7 +4,7 @@ process GATK4_VARIANTFILTRATION { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index a679c2f39dc..ea846e1d539 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,7 +4,7 @@ process GATK4_VARIANTRECALIBRATOR { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index 2a5cf5d071e..1d51b47fcb4 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -4,7 +4,7 @@ process GECCO_RUN { conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) def container_image = "/gecco:0.9.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(hmm) diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 08f78f298bd..87c4323d747 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -4,7 +4,7 @@ process GENMAP_INDEX { conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) def container_image = "/genmap:1.3.0--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index a2249f1cdce..b708dac4f53 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -4,7 +4,7 @@ process GENMAP_MAPPABILITY { conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) def container_image = "/genmap:1.3.0--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index bb9f0934d55..f99f35b8596 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -4,7 +4,7 @@ process GENMOD_ANNOTATE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index ae8647a633d..6bd55a0d208 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -4,7 +4,7 @@ process GENMOD_COMPOUND { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 97e05b226a1..3803e81a429 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -4,7 +4,7 @@ process GENMOD_MODELS { conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index dca44cda3af..0fa66dfb7dd 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -4,7 +4,7 @@ process GENMOD_SCORE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index 6b435ba39bf..d55d4d08354 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -4,7 +4,7 @@ process GENOMESCOPE2 { conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) def container_image = "/genomescope2:2.0--py310r41hdfd78af_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index 60d943fc213..2cfc25c0923 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -4,7 +4,7 @@ process GENOTYPHI_PARSE { conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) def container_image = "/genotyphi:1.9.1--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 1346ea5508c..554a5e7bc5a 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -4,7 +4,7 @@ process GENRICH { conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) def container_image = "/genrich:0.6.1--h5bf99c6_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(treatment_bam) diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index d3c66e4d606..36fbed6ca3d 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -5,7 +5,7 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) def container_image = "/gfaffix:0.1.4--hec16e2b_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index db8cf75a7cf..a424fb2faa7 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -4,7 +4,7 @@ process GFFREAD { conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) def container_image = "/gffread:0.12.1--h8b12597_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index 6f18132bcf3..ca1912436ac 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -4,7 +4,7 @@ process GLIMPSE_CHUNK { conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) def container_image = "/glimpse-bio:1.1.1--h2ce4488_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index c92fdedebc1..2babb3c4e20 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -4,7 +4,7 @@ process GLNEXUS { conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) def container_image = "/glnexus:1.4.1--h40d77a6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index 6e0314cd4be..c3bfbd2ffc4 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -4,7 +4,7 @@ process GOAT_TAXONSEARCH { conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) def container_image = "/goat:0.2.0--h92d785c_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index cf89fafe0e4..2855702df94 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -5,7 +5,7 @@ process GRAPHMAP2_ALIGN { conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) def container_image = "/graphmap:0.6.3--he513fc3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index 79cd43f4e7d..d1e26119469 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -3,7 +3,7 @@ process GRAPHMAP2_INDEX { conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) def container_image = "/graphmap:0.6.3--he513fc3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index a57f78ec13b..0398432537e 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -4,7 +4,7 @@ process GSTAMA_COLLAPSE { conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) def container_image = "/gs-tama:1.0.3--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index d34211e9839..e4346c0c89f 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -4,7 +4,7 @@ process GSTAMA_MERGE { conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) def container_image = "/gs-tama:1.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index b01e0c26bd3..76681213343 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -4,7 +4,7 @@ process GSTAMA_POLYACLEANUP { conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) def container_image = "/gs-tama:1.0.3--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 403206977c9..631b4dda46c 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -5,7 +5,7 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) def container_image = "/gtdbtk:1.5.0--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path("bins/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 278f12d723f..f26603cf300 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -3,7 +3,7 @@ process GUBBINS { conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) def container_image = "/gubbins:3.0.0--py39h5bf99c6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 552cca2be7e..46769db6c03 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -4,7 +4,7 @@ process GUNC_DOWNLOADDB { conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) def container_image = "/gunc:1.0.5--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index 1578021e5d6..b0ca3ff303b 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -4,7 +4,7 @@ process GUNC_RUN { conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) def container_image = "/gunc:1.0.5--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 33929b1ab1d..5542a071317 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -4,7 +4,7 @@ process GUNZIP { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index 368d47126a0..917c04db1ae 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -4,7 +4,7 @@ process GVCFTOOLS_EXTRACTVARIANTS { conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) def container_image = "/gvcftools:0.17.0--he941832_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index d80d71f2d24..8b5507fa698 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -4,7 +4,7 @@ process HAMRONIZATION_ABRICATE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index 0d29d46a368..a1452c239e8 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -4,7 +4,7 @@ process HAMRONIZATION_AMRFINDERPLUS { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index cd78db54f6f..552d8de6f03 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -4,7 +4,7 @@ process HAMRONIZATION_DEEPARG { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index 639b09e844a..03ad24392c2 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -4,7 +4,7 @@ process HAMRONIZATION_FARGENE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index e0687d4140f..ed7d435636c 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -4,7 +4,7 @@ process HAMRONIZATION_RGI { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index 0c4d78b1897..0b72b6a51d3 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -3,7 +3,7 @@ process HAMRONIZATION_SUMMARIZE { conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path(reports) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index ca023330571..c5b261f6721 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -4,7 +4,7 @@ process HAPLOCHECK { conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) def container_image = "/haplocheck:1.3.3--h4a94de4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 0e5e1b72bca..137c84e9990 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -4,7 +4,7 @@ process HAPLOGREP2_CLASSIFY { conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) def container_image = "/haplogrep:2.4.0--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index b67e35cc1e6..66960c60d6d 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -5,7 +5,7 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index 4ab843eb197..d161346365f 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -5,7 +5,7 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(bed) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 6410050c263..6d2d8e9b678 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -4,7 +4,7 @@ process HICAP { conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) def container_image = "/hicap:1.0.3--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index 048095bc438..f9fce1e2647 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -4,7 +4,7 @@ process HIFIASM { conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) def container_image = "/hifiasm:0.15.4--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 790abfb14a8..32128fd0f71 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -5,7 +5,7 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 25addfb210a..601c1fa6ead 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -6,7 +6,7 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) def container_image = "/hisat2:2.2.1--h1b792b2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 7aa0fb4b687..caaeab906ab 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -5,7 +5,7 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) def container_image = "/hisat2:2.2.1--h1b792b2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 9ac135559b6..4e436c0d761 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -4,7 +4,7 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index cb06b02570b..117b4001c83 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -5,7 +5,7 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 8cca042e7d8..21de1a0b138 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -4,7 +4,7 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 1e39cd3c3dc..5e0247dfbc0 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -5,7 +5,7 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index a044208d865..bdac0bdde16 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -4,7 +4,7 @@ process HMMER_ESLALIMASK { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index c333f6b2926..93d30d16e72 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -4,7 +4,7 @@ process HMMER_ESLREFORMAT { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index d93c4e2864f..f1c812e83b4 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -4,7 +4,7 @@ process HMMER_HMMALIGN { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 7ec3c106b99..ad24da5ff2f 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -4,7 +4,7 @@ process HMMER_HMMBUILD { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h87f3376_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 5d1f0a30440..d60a2986a7e 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -4,7 +4,7 @@ process HMMER_HMMSEARCH { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index 4bd8ed42232..ed1ba06903a 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -4,7 +4,7 @@ process HMTNOTE { conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) def container_image = "/hmtnote:0.7.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 6780afd09fa..e680036e6e3 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -5,7 +5,7 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 97246ff570f..257582505d1 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -5,7 +5,7 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 77264b39861..85836267a61 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -6,7 +6,7 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) def container_image = "/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 18fe039056f..9e955846a24 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -5,7 +5,7 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index d60443af644..5da6aa425e9 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -5,7 +5,7 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index bbc784513c0..17b3ee86586 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -5,7 +5,7 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) def container_image = "/hpsuissero%3A1.0.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index ec4e5f5ce56..afa8a6c1132 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -4,7 +4,7 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path wigs diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index 85e81f023d1..41d79e34f50 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -5,7 +5,7 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index 9ecf0f50353..bcd2df13f7f 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -4,7 +4,7 @@ process IDR { conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) def container_image = "/idr:2.0.4.2--py39hcbe4a3b_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path peaks diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index d9e21ce3032..b035008f471 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -4,7 +4,7 @@ process INSTRAIN_PROFILE { conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) def container_image = "/instrain:1.6.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index a68b93fd8df..d77eb19bff0 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -4,7 +4,7 @@ process IQTREE { conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) def container_image = "/iqtree:2.1.4_beta--hdcc8f71_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index cf65f31bd8d..4908ddbfa23 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -4,7 +4,7 @@ process ISMAPPER { conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) def container_image = "/ismapper:2.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index fa2616829cd..344492a6435 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -4,7 +4,7 @@ process ISOSEQ3_CLUSTER { conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) def container_image = "/isoseq3:3.4.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index c8f62a37069..b4c2f5ababc 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -4,7 +4,7 @@ process ISOSEQ3_REFINE { conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) def container_image = "/isoseq3:3.4.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 58c4f14146f..1021049f82e 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -4,7 +4,7 @@ process IVAR_CONSENSUS { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) def container_image = "/ivar:1.3.1--h089eab3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index 117051e6a46..c722e345cc2 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -4,7 +4,7 @@ process IVAR_TRIM { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) def container_image = "/ivar:1.3.1--h089eab3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index c405c421a1b..c8c4b9c21ef 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -4,7 +4,7 @@ process IVAR_VARIANTS { conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) def container_image = "/ivar:1.3.1--h089eab3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index 35033df729e..62ba820adff 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -9,7 +9,7 @@ process JUPYTERNOTEBOOK { //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) def container_image = "/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index 747b280d48d..242c1af4417 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -4,7 +4,7 @@ process KAIJU_KAIJU { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) def container_image = "/kaiju:1.8.2--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 58fe1496d58..8c1cd5058af 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -4,7 +4,7 @@ process KAIJU_KAIJU2KRONA { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) def container_image = "/kaiju:1.8.2--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index e32a8da1111..cec631ce376 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -4,7 +4,7 @@ process KAIJU_KAIJU2TABLE { conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) def container_image = "/kaiju:1.8.2--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(results) diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index b98490e6639..e073cd0eca0 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -4,7 +4,7 @@ process KALLISTO_INDEX { conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) def container_image = "/kallisto:0.46.2--h4f7b962_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index ef749679111..6b1feb1b829 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -4,7 +4,7 @@ process KALLISTOBUSTOOLS_COUNT { conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) def container_image = "/kb-python:0.27.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 24cc1154d71..d5a23179076 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -4,7 +4,7 @@ process KALLISTOBUSTOOLS_REF { conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) def container_image = "/kb-python:0.27.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 75188917032..9cc399f5614 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -4,7 +4,7 @@ process KAT_HIST { conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) def container_image = "/kat:2.4.2--py38hfc5f9d8_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index faf991fef1a..fee17545287 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -4,7 +4,7 @@ process KHMER_NORMALIZEBYMEDIAN { conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) def container_image = "/khmer:3.0.0a3--py37haa7609a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path pe_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 74bc1182f9f..8bf7d4e2bbd 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -4,7 +4,7 @@ process KHMER_UNIQUEKMERS { conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) def container_image = "/khmer:3.0.0a3--py37haa7609a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index afec47d2b23..c11de5b950a 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -4,7 +4,7 @@ process KLEBORATE { conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) def container_image = "/kleborate:2.1.0--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 28a94be9a13..33501024448 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -4,7 +4,7 @@ process KRAKEN2_KRAKEN2 { conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) def container_image = "/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index afe56201a88..47f8f363ce6 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -3,7 +3,7 @@ process KRAKENTOOLS_COMBINEKREPORTS { conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) def container_image = "/krakentools:1.2--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index d9c7cfad61f..52109a176c8 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -5,7 +5,7 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) def container_image = "/krakentools:1.2--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index ceb618035e0..8dd177b4808 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -5,7 +5,7 @@ process KRONA_KRONADB { conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) def container_image = "/krona:2.7.1--pl526_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 706cf9bf138..23a24114281 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -5,7 +5,7 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) def container_image = "/krona:2.8--pl5262hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 78655353618..042467dfb9e 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -4,7 +4,7 @@ process KRONA_KTIMPORTTEXT { conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) def container_image = "/krona:2.8.1--pl5321hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index 34b2dea3a03..089f46754b0 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -5,7 +5,7 @@ process KRONA_KTUPDATETAXONOMY { conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) def container_image = "/krona:2.7.1--pl526_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 7999fbd5a74..e6b5abb00ef 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -4,7 +4,7 @@ process LAST_DOTPLOT { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 767c35d32d4..e00910370f3 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -4,7 +4,7 @@ process LAST_LASTAL { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index ae602410baa..c50b91e70c7 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -4,7 +4,7 @@ process LAST_LASTDB { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 10a432ec2f3..08e3852fa17 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -4,7 +4,7 @@ process LAST_MAFCONVERT { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index f091dd3d377..e125af0f4ed 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -4,7 +4,7 @@ process LAST_MAFSWAP { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index dc5e8af88cf..93a6f8d64a6 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -4,7 +4,7 @@ process LAST_POSTMASK { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 09e4d2dbac6..058a225c0da 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -4,7 +4,7 @@ process LAST_SPLIT { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 00aec540fcf..187be436146 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -4,7 +4,7 @@ process LAST_TRAIN { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index 680a2684908..40b38d52cd1 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -5,7 +5,7 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) def container_image = "/leehom:1.2.15--h29e30f7_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index a3ee06ec833..d6e2a8ea918 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -4,7 +4,7 @@ process LEGSTA { conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) def container_image = "/legsta%3A0.5.1--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index f68781782c1..2226a2050dd 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -4,7 +4,7 @@ process LIMA { conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) def container_image = "/lima:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ccs) diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index 056f0425e66..3a906448391 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -4,7 +4,7 @@ process LISSERO { conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) def container_image = "/lissero:0.4.9--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index a621dfa26c3..2036fe4dfbe 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -4,7 +4,7 @@ process LOFREQ_CALL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 49f5eb81d6c..8ee1ae76c6b 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -4,7 +4,7 @@ process LOFREQ_CALLPARALLEL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index 39323b1bc71..32cb7988e0d 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -4,7 +4,7 @@ process LOFREQ_FILTER { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 4e2b5945984..64a2d219355 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -4,7 +4,7 @@ process LOFREQ_INDELQUAL { conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 1f6ff4338b4..0df58d5777f 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -4,7 +4,7 @@ process MACREL_CONTIGS { conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) def container_image = "/macrel:1.1.0--py36hc5360cc_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 9f6b0d3ea12..5e370924dc4 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -4,7 +4,7 @@ process MACS2_CALLPEAK { conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) def container_image = "/macs2:2.2.7.1--py38h4a8c8d9_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index a64a59f92ca..aa001be3b07 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -4,7 +4,7 @@ process MAFFT { conda (params.enable_conda ? "bioconda::mafft=7.490" : null) def container_image = "/mafft:7.490--h779adbc_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 6e671571b9b..93937a00747 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -4,7 +4,7 @@ process MALT_BUILD { conda (params.enable_conda ? "bioconda::malt=0.41" : null) def container_image = "/malt:0.41--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fastas diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index 6e22ed77e3a..ec1425677c1 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -4,7 +4,7 @@ process MALT_RUN { conda (params.enable_conda ? "bioconda::malt=0.41" : null) def container_image = "/malt:0.41--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastqs) diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index 2c506373e64..02ed042676b 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -4,7 +4,7 @@ process MALTEXTRACT { conda (params.enable_conda ? "bioconda::hops=0.35" : null) def container_image = "/hops:0.35--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path rma6 diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 02f36af4e04..8397f96dee2 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -4,7 +4,7 @@ process MANTA_CONVERTINVERSION { conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 3c6bea97519..9aea35649d1 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -4,7 +4,7 @@ process MANTA_GERMLINE { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) def container_image = "/manta:1.6.0--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 7b9c145bd42..9fc249e535f 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -4,7 +4,7 @@ process MANTA_SOMATIC { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) def container_image = "/manta:1.6.0--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index b154e6a3363..e6790a9f14c 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -4,7 +4,7 @@ process MANTA_TUMORONLY { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) def container_image = "/manta:1.6.0--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index 928c77b5430..ca81c395f77 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -4,7 +4,7 @@ process MAPDAMAGE2 { conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) def container_image = "/mapdamage2:2.2.1--pyr40_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index 62c49d99a22..3d2d872603c 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -4,7 +4,7 @@ process MASH_DIST { conda (params.enable_conda ? "bioconda::mash=2.3" : null) def container_image = "/mash:2.3--he348c14_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 970d8f581ef..97b02c79910 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -4,7 +4,7 @@ process MASH_SCREEN { conda (params.enable_conda ? "bioconda::mash=2.3" : null) def container_image = "/mash:2.3--he348c14_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 3c73caae75c..24515e3b9d6 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -3,7 +3,7 @@ process MASH_SKETCH { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) def container_image = "/mash:2.3--he348c14_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index e28a310af8c..f22bfa7390f 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -4,7 +4,7 @@ process MASHTREE { conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) def container_image = "/mashtree:1.2.0--pl526h516909a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index eb7f0d3f20e..cdfabad70d5 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -4,7 +4,7 @@ process MAXBIN2 { conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) def container_image = "/maxbin2:2.2.7--he1b5a44_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index ece94cdae68..55e603f79b1 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -2,7 +2,7 @@ process MAXQUANT_LFQ { tag "$meta.id" label 'process_long' conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null) - container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" + container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" } else { } diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index b5466936ee9..224ae3ec9c1 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -5,7 +5,7 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) def container_image = "/mcroni%3A1.0.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index 60c450bf0cb..5471b2ba310 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -4,7 +4,7 @@ process MD5SUM { conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index c81adee639e..bf42c9b845a 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -4,7 +4,7 @@ process MEDAKA { conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) def container_image = "/medaka:1.4.4--py38h130def0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 18948cc136c..3692eaacd6a 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -4,7 +4,7 @@ process MEGAHIT { conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) def container_image = "/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index f293e1ffa36..08269dabce0 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -4,7 +4,7 @@ process MEGAN_DAA2INFO { conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) def container_image = "/megan:6.21.7--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(daa) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 32b4e892167..a977bd65ac1 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -4,7 +4,7 @@ process MEGAN_RMA2INFO { conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) def container_image = "/megan:6.21.7--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index 619f9307f6f..c86c107c278 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -4,7 +4,7 @@ process MENINGOTYPE { conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) def container_image = "/meningotype:0.8.5--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index ab78fa8e484..b9eb1a8de4e 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -4,7 +4,7 @@ process MERQURY { conda (params.enable_conda ? "bioconda::merqury=1.3" : null) def container_image = "/merqury:1.3--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index ece88013b4b..b7f72b49304 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -4,7 +4,7 @@ process MERYL_COUNT { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) def container_image = "/meryl:1.3--h87f3376_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 7b3c1198d27..8d6de50f91c 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -4,7 +4,7 @@ process MERYL_HISTOGRAM { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) def container_image = "/meryl:1.3--h87f3376_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 37e6f2fdbf1..9e2b0dfeacd 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -4,7 +4,7 @@ process MERYL_UNIONSUM { conda (params.enable_conda ? "bioconda::meryl=1.3" : null) def container_image = "/meryl:1.3--h87f3376_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 64799adb018..6daec895952 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -4,7 +4,7 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) def container_image = "/metabat2:2.15--h986a166_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index b59190ea0d9..8318eda35e2 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -4,7 +4,7 @@ process METABAT2_METABAT2 { conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) def container_image = "/metabat2:2.15--h986a166_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 69db3e0be47..a333e6a776c 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -3,7 +3,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 8f47737964f..505d24ff48d 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -4,7 +4,7 @@ process METAPHLAN3_METAPHLAN3 { conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 7aeb848ae1d..1a762880673 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -4,7 +4,7 @@ process METHYLDACKEL_EXTRACT { conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) def container_image = "/methyldackel:0.6.0--h22771d5_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index f8f001d4bef..7ba33944c62 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -4,7 +4,7 @@ process METHYLDACKEL_MBIAS { conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) def container_image = "/methyldackel:0.6.0--h22771d5_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 5a13d41a732..cb5b6df306d 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,7 @@ process MINIA { conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) def container_image = "/minia:3.2.6--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 6a2acd52e2c..cfff80b718e 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -4,7 +4,7 @@ process MINIASM { conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) def container_image = "/miniasm:0.3_r179--h5bf99c6_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index ca0dc96e522..ddd1d2fe61d 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -4,7 +4,7 @@ process MINIMAP2_ALIGN { conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) def container_image = "/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 9a689e72971..955eb0da515 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -3,7 +3,7 @@ process MINIMAP2_INDEX { conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) def container_image = "/minimap2:2.21--h5bf99c6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 393b959025e..2d1ee12b85a 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -4,7 +4,7 @@ process MLST { conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) def container_image = "/mlst:2.19.0--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index 2c5b48b8a4f..f2c88f29381 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -4,7 +4,7 @@ process MOBSUITE_RECON { conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) def container_image = "/mob_suite%3A3.0.3--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index ee80fb8276b..fe54ed4453d 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,7 +4,7 @@ process MOSDEPTH { conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) def container_image = "/mosdepth:0.3.3--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index 2a5c25cac4c..e459d3e8311 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -3,7 +3,7 @@ process MOTUS_DOWNLOADDB { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) def container_image = "/motus:3.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 075362bca68..17e5fb35f14 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -6,7 +6,7 @@ process MOTUS_MERGE { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) def container_image = "/motus:3.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index 3b9ce2ac5fc..e3554e1ce3e 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -4,7 +4,7 @@ process MOTUS_PROFILE { conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) def container_image = "/motus:3.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index ab8659f35ec..ce8734fc98a 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -4,7 +4,7 @@ process MSISENSOR_MSI { conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) def container_image = "/msisensor:0.5--hb3646a4_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index 6adeb96538f..ce6dd3eac7c 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -4,7 +4,7 @@ process MSISENSOR_SCAN { conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) def container_image = "/msisensor:0.5--hb3646a4_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index 69b5b28622d..c55313c3700 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -4,7 +4,7 @@ process MSISENSOR2_MSI { conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) def container_image = "/msisensor2:0.1--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index f44ff3bb463..a9a5e413ce6 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -4,7 +4,7 @@ process MSISENSOR2_SCAN { conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) def container_image = "/msisensor2:0.1--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index da124b8ba6f..85531a75783 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -4,7 +4,7 @@ process MSISENSORPRO_MSI_SOMATIC { conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index a549999999c..f60a31e36e0 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -4,7 +4,7 @@ process MSISENSORPRO_SCAN { conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index 14714850ef5..7d854012c8c 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -4,7 +4,7 @@ process MTNUCRATIO { conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) def container_image = "/mtnucratio:0.7--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 6cc80edff3e..74a559a448d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,7 +3,7 @@ process MULTIQC { conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) def container_image = "/multiqc:1.13--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 3fa20d68ea3..78bca1a5b77 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -4,7 +4,7 @@ process MULTIVCFANALYZER { conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) def container_image = "/multivcfanalyzer:0.85.2--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index 4ecb10f2aaa..c1fa75e8f86 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -5,7 +5,7 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) def container_image = "/mummer:3.23--pl5262h1b792b2_12" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 07c7cc087ad..d41467933b5 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -4,7 +4,7 @@ process MUSCLE { conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) def container_image = "/muscle:3.8.1551--h7d875b9_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index 5d682d727d4..38316f80a68 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -4,7 +4,7 @@ process MYKROBE_PREDICT { conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) def container_image = "/mykrobe:0.11.0--py39h2add14b_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 66014fbd18c..3626e3c2e61 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -4,7 +4,7 @@ process NANOLYSE { conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) def container_image = "/nanolyse:1.2.0--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index 01fb5f33ed8..ad7d30ca7da 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -4,7 +4,7 @@ process NANOPLOT { conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) def container_image = "/nanoplot:1.40.0--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index 858ae2387de..69539b07204 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -4,7 +4,7 @@ process NCBIGENOMEDOWNLOAD { conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) def container_image = "/ncbi-genome-download:0.3.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val meta diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 03f2a8280a8..cb9d0e58f87 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -4,7 +4,7 @@ process NEXTCLADE_DATASETGET { conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) def container_image = "/nextclade:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 64496533c39..7ef8f630cb7 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -4,7 +4,7 @@ process NEXTCLADE_RUN { conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) def container_image = "/nextclade:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index 0787e747ac7..c4ed5755d4d 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -4,7 +4,7 @@ process NEXTGENMAP { conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) def container_image = "/nextgenmap%3A0.5.5--hc9558a2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index 718f99cb02e..08d96c13ec5 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -4,7 +4,7 @@ process NGMASTER { conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) def container_image = "/ngmaster:0.5.8--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 9d7944575a0..b814d8836ca 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -3,7 +3,7 @@ process NGSCHECKMATE_NCM { conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) def container_image = "/ngscheckmate:1.0.0--py27r41hdfd78af_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path files diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index c69b6ebb55f..3844fd95f1c 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -4,7 +4,7 @@ process NUCMER { conda (params.enable_conda ? "bioconda::mummer=3.23" : null) def container_image = "/mummer:3.23--pl5262h1b792b2_12" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 0b4ee308b04..68db773c69c 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -4,7 +4,7 @@ process OPTITYPE { conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) def container_image = "/optitype:1.3.5--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index 19dd2dc0846..59150c677fe 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -4,7 +4,7 @@ process PAIRIX { conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) def container_image = "/pairix:0.3.7--py36h30a8e3e_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index e4fc4feab01..b782a287d79 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -4,7 +4,7 @@ process PAIRTOOLS_DEDUP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 0c6805c4292..a717e281b52 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -4,7 +4,7 @@ process PAIRTOOLS_FLIP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index f49f1881025..33c8d73f106 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -4,7 +4,7 @@ process PAIRTOOLS_PARSE { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 1684e6d2936..7b4211a899e 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -4,7 +4,7 @@ process PAIRTOOLS_RESTRICT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pairs) diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index 67a566d9670..ec00eddd00f 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -4,7 +4,7 @@ process PAIRTOOLS_SELECT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index 0aa3db2c37f..cb4ffcdf184 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -4,7 +4,7 @@ process PAIRTOOLS_SORT { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index 3d9a013f76a..f892bff44f4 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -4,7 +4,7 @@ process PANAROO_RUN { conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) def container_image = "/panaroo:1.2.9--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 8aa629eab8f..7e4fc5baeb8 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -4,7 +4,7 @@ process PANGOLIN { conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) def container_image = "/pangolin:4.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index 8b90b62fe95..8a6a7485f90 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -5,7 +5,7 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) def container_image = "/paraclu:10--h9a82719_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 6936b1a7ce8..09f1b2873e2 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -4,7 +4,7 @@ process PASTY { conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) def container_image = "/pasty:1.0.0--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index 0da8e9e174b..7fd452dd425 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -4,7 +4,7 @@ process PBBAM_PBMERGE { conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) def container_image = "/pbbam:1.7.0--h058f120_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index d9ed988b69f..47e12094a59 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -4,7 +4,7 @@ process PBCCS { conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) def container_image = "/pbccs:6.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(pbi) diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 28935b1295f..745aaca77c8 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -4,7 +4,7 @@ process PBPTYPER { conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) def container_image = "/pbptyper:1.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index b4a8ac39e1a..45b9db5929d 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -4,7 +4,7 @@ process PEAR { conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) def container_image = "/pear:0.9.6--h67092d7_8" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index 0f5344c671b..e70c88cd8e8 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -4,7 +4,7 @@ process PEDDY { conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) def container_image = "/peddy:0.4.8--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 9998b800799..89b046cf1d8 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -5,7 +5,7 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) def container_image = "/phantompeakqualtools:1.2.2--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index ab70a3b5ce4..630991f8414 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -4,7 +4,7 @@ process PHYLOFLASH { conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) def container_image = "/phyloflash:3.4--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 5bd44aeb31f..42103a93f3c 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -4,7 +4,7 @@ process PICARD_ADDORREPLACEREADGROUPS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 786790038e1..3f756092fae 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -4,7 +4,7 @@ process PICARD_CLEANSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index ed5092aca9d..328cca815e5 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -4,7 +4,7 @@ process PICARD_COLLECTHSMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index c19ea982ebb..9834b697db3 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -4,7 +4,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 9d1a69bfa5e..bab23c6d5c7 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -4,7 +4,7 @@ process PICARD_COLLECTWGSMETRICS { conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 4585cf2c626..8ebfa337728 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -4,7 +4,7 @@ process PICARD_CREATESEQUENCEDICTIONARY { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index 6509b2604c4..97265ef2147 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -4,7 +4,7 @@ process PICARD_CROSSCHECKFINGERPRINTS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input1) diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index e42b0501eda..8ca715f6990 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -4,7 +4,7 @@ process PICARD_FASTQTOSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index c68307d4cd4..c2ed6354b0f 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -4,7 +4,7 @@ process PICARD_FILTERSAMREADS { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index edbe6c9c13e..e173fa8a330 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -4,7 +4,7 @@ process PICARD_FIXMATEINFORMATION { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 06c178ccb2b..95bcc090602 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -4,7 +4,7 @@ process PICARD_LIFTOVERVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 6ada3065bb7..ae01fcf6e82 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,7 +4,7 @@ process PICARD_MARKDUPLICATES { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index b50fb3033e8..6390fd687ae 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -4,7 +4,7 @@ process PICARD_MERGESAMFILES { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 3b4f76088e2..b26d6630447 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -5,7 +5,7 @@ process PICARD_RENAMESAMPLEINVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index e5048fd96a3..e2288e15e5f 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -4,7 +4,7 @@ process PICARD_SORTSAM { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 7e39895e5a5..1a7aba1bfa2 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -4,7 +4,7 @@ process PICARD_SORTVCF { conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index b6f4442c6c7..0cdd2e4d9de 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -4,7 +4,7 @@ process PINTS_CALLER { conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) def container_image = "/pypints:1.1.6--pyh5e36f6f_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index e875286daf4..7628016a3f0 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -4,7 +4,7 @@ process PIRATE { conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) def container_image = "/pirate:1.0.4--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index 281f61edac4..c99139a9077 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -5,7 +5,7 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) def container_image = "/plasmidfinder:2.1.6--py310hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index 857739c5c23..c3cf0219077 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -4,7 +4,7 @@ process PLASMIDID { conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) def container_image = "/plasmidid:1.6.5--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index fdf98899e61..39ff25c52d3 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -4,7 +4,7 @@ process PLINK_EXTRACT { conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) def container_image = "/plink:1.90b6.21--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index 4a891f8eaeb..b0848c46850 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -4,7 +4,7 @@ process PLINK_VCF { conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) def container_image = "/plink:1.90b6.21--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index bd2abcf3725..bb3f4d43560 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -4,7 +4,7 @@ process PLINK2_EXTRACT { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) def container_image = "/plink2:2.00a2.3--h712d239_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index 88d69810433..82fe2d3879a 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -4,7 +4,7 @@ process PLINK2_SCORE { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) def container_image = "/plink2:2.00a2.3--h712d239_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(pgen), path(psam), path(pvar) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index e3c7e24693e..852ffabb14a 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -4,7 +4,7 @@ process PLINK2_VCF { conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) def container_image = "/plink2:2.00a2.3--h712d239_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 609408910da..88bcaf2abee 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -4,7 +4,7 @@ process PMDTOOLS_FILTER { conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) def container_image = "/pmdtools:0.60--hdfd78af_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path (bai) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index 6bfbf9c1982..db6ec83efd1 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -4,7 +4,7 @@ process PORECHOP { conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) def container_image = "/porechop:0.2.4--py39h7cff6ad_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 3df01db792a..8cb57b9b82b 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -5,7 +5,7 @@ process PRESEQ_CCURVE { conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) def container_image = "/preseq:3.1.2--h445547b_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 38ca6912ec5..808da135299 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -5,7 +5,7 @@ process PRESEQ_LCEXTRAP { conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) def container_image = "/preseq:3.1.2--h445547b_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index 3e2618a5d57..862e6b29862 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -4,7 +4,7 @@ process PRINSEQPLUSPLUS { conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) def container_image = "/prinseq-plus-plus:1.2.3--hc90279e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 114391e1dd4..3c6b9c9504f 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -4,7 +4,7 @@ process PRODIGAL { conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) def container_image = "/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 1d4085f2280..eebc73ab336 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -4,7 +4,7 @@ process PROKKA { conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) def container_image = "/prokka%3A1.14.6--pl5321hdfd78af_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index fe1ad718090..e28f13c1f8d 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -4,7 +4,7 @@ process PYCOQC { conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) def container_image = "/pycoqc:2.5.2--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index ecda2a3b46f..359f1f42828 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -4,7 +4,7 @@ process PYDAMAGE_ANALYZE { conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) def container_image = "/pydamage:0.70--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index 1a8be87ec58..231f2b7b2ca 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -4,7 +4,7 @@ process PYDAMAGE_FILTER { conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) def container_image = "/pydamage:0.70--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index e13a85ea201..39e0bce88fc 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -4,7 +4,7 @@ process QCAT { conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) def container_image = "/qcat:1.1.0--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 9d2c9c0534b..6babc701872 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -4,7 +4,7 @@ process QUALIMAP_BAMQC { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) def container_image = "/qualimap:2.2.2d--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 0dc68fd70bc..fef20f20fc8 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -4,7 +4,7 @@ process QUALIMAP_BAMQCCRAM { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(cram), path(crai) diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 73d0392e1c0..128eed9acdd 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -4,7 +4,7 @@ process QUALIMAP_RNASEQ { conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) def container_image = "/qualimap:2.2.2d--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index d7bb08ef288..27a127b39f8 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -3,7 +3,7 @@ process QUAST { conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) def container_image = "/quast:5.2.0--py39pl5321h2add14b_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path consensus diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index d1b62b2bf79..b5ded55141f 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -4,7 +4,7 @@ process RACON { conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) def container_image = "/racon:1.4.20--h9a82719_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 6fb5f8db687..a7662a2f85d 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -4,7 +4,7 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) def container_image = "/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index a24fe59ecb4..8f9c5130b7b 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -4,7 +4,7 @@ process RASUSA { conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) def container_image = "/rasusa:0.3.0--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads), val(genome_size) diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index c6ae348516d..3baae4df403 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -4,7 +4,7 @@ process RAVEN { conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) def container_image = "/raven-assembler:1.6.1--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index ddbbb45e159..c950c45b728 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -3,7 +3,7 @@ process RAXMLNG { conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) def container_image = "/raxml-ng:1.0.3--h32fcf60_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index db4ad2edf9f..763d8ae2c2e 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -4,7 +4,7 @@ process RGI_MAIN { conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) def container_image = "/rgi:5.2.1--pyha8f3691_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 6098705fe71..c516292d4b8 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -4,7 +4,7 @@ process RHOCALL_ANNOTATE { conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) def container_image = "/rhocall:0.5.1--py39hbf8eff0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 719b3f016d0..7753f61fa0e 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -9,7 +9,7 @@ process RMARKDOWNNOTEBOOK { //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) def container_image = "/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index c1816e15dd8..1eec1d9f8e3 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -4,7 +4,7 @@ process ROARY { conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) def container_image = "/roary:3.13.0--pl526h516909a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index ba22da6d381..d0dfc33585c 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -4,7 +4,7 @@ process RSEM_CALCULATEEXPRESSION { conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 56b20bdf1bc..fde8eb88ed6 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -4,7 +4,7 @@ process RSEM_PREPAREREFERENCE { conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta, stageAs: "rsem/*" diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index e8ba91135b2..e27f11bbb4d 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -4,7 +4,7 @@ process RSEQC_BAMSTAT { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index 32834be468e..c401c2fc3e7 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -4,7 +4,7 @@ process RSEQC_INFEREXPERIMENT { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index cf03eaeaf1d..40fb8331eab 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -4,7 +4,7 @@ process RSEQC_INNERDISTANCE { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index f2a4efb0716..e3e50b4b5ba 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -4,7 +4,7 @@ process RSEQC_JUNCTIONANNOTATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 128cd204c66..382a7a59cde 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -4,7 +4,7 @@ process RSEQC_JUNCTIONSATURATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index 98b0f02febe..3c7ef15271c 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -4,7 +4,7 @@ process RSEQC_READDISTRIBUTION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 61949337a7b..b8fcacc86d5 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -4,7 +4,7 @@ process RSEQC_READDUPLICATION { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 3866400af5c..645b165f239 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -4,7 +4,7 @@ process RSEQC_TIN { conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 7a0d68cf700..6024b164b7b 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -4,7 +4,7 @@ process RTGTOOLS_PEDFILTER { conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) def container_image = "/rtg-tools:3.12.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index ed83c042e07..2eac07bb63a 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -4,7 +4,7 @@ process RTGTOOLS_VCFEVAL { conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) def container_image = "/rtg-tools:3.12.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index a0a58ecf773..f7efcf6144c 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -4,7 +4,7 @@ process SALMON_INDEX { conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) def container_image = "/salmon:1.5.2--h84f40af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path genome_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index f8ef268682a..7d48f97dedb 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -4,7 +4,7 @@ process SALMON_QUANT { conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) def container_image = "/salmon:1.5.2--h84f40af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 6160226df87..736ea1f879e 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -4,7 +4,7 @@ process SAMBLASTER { conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index f82be398f76..9075c9252f5 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_AMPLICONCLIP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index 82907463fc2..e251d6dd268 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_BAM2FQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 3d88d3c6940..c2ad471d591 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_COLLATE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 3631069fdd4..2c2997cc676 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_COLLATEFASTQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 0aa10559505..5a435765887 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_CONVERT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 3a7424fe2fc..74c4a313b1a 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_DEPTH { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 9975271a78c..6b27f658a80 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_DICT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index d61a38cf67b..9f3d2de1138 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_FAIDX { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 186b59e0b03..798f4e66250 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_FASTA { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 2afbbef0b31..65e755be9ee 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_FASTQ { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 6e85fab7c70..4a4b4271a27 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_FIXMATE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 84f866ae5a0..e6a6dfb66fc 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_FLAGSTAT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index aa054eff8b6..f98c9b5f928 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_GETRG { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 24f8ddc3a7d..2aabfe8e69d 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_IDXSTATS { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 6da574867a9..d20b72da0ad 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_INDEX { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 473e5ebd726..5483ae11867 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_MARKDUP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 71efca897ec..979bcf0b834 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_MERGE { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index d9e9d8ffab6..47ecd071026 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_MPILEUP { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index e2aeb48080d..c12227f1255 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_SORT { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 406016bafc3..3e4c2c877b9 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_STATS { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index db26333be22..603f9ad8a4d 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,7 +4,7 @@ process SAMTOOLS_VIEW { conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index afcfe794652..b546a108088 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -4,7 +4,7 @@ process SCOARY { conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) def container_image = "/scoary:1.6.16--py_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index 7307ad93f97..7d3dd518e1c 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -4,7 +4,7 @@ process SCRAMBLE_CLUSTERANALYSIS { conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) def container_image = "/scramble:1.0.1--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(clusters) diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 88f00cd761d..e5bc472d659 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -4,7 +4,7 @@ process SCRAMBLE_CLUSTERIDENTIFIER { conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) def container_image = "/scramble:1.0.1--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index b26f6b81c90..f1987432015 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -5,7 +5,7 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) def container_image = "/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 90bb690350b..a83a5f97732 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -4,7 +4,7 @@ process SEQKIT_PAIR { conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) def container_image = "/seqkit:2.1.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index c13542b4ff2..6944c42312d 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -4,7 +4,7 @@ process SEQKIT_REPLACE { conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) def container_image = "/seqkit:2.1.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index fdd80164917..4e05035e5a6 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -4,7 +4,7 @@ process SEQKIT_SPLIT2 { conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) def container_image = "/seqkit:2.1.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index f00abcaf52e..e7956607b1b 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -4,7 +4,7 @@ process SEQKIT_STATS { conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) def container_image = "/seqkit:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index 771bd2725bf..060cb50a05b 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -4,7 +4,7 @@ process SEQSERO2 { conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) def container_image = "/seqsero2:1.2.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index ebdf56c0d97..9edeb97784a 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -4,7 +4,7 @@ process SEQTK_MERGEPE { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index b0f0864124a..62814a8e198 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -4,7 +4,7 @@ process SEQTK_RENAME { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index c2b5d6bd2b2..2c114b44e28 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -4,7 +4,7 @@ process SEQTK_SAMPLE { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 9258458bb1d..209229cf461 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -4,7 +4,7 @@ process SEQTK_SEQ { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index d8c1cf66342..3c38cdd3b86 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -4,7 +4,7 @@ process SEQTK_SUBSEQ { conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path sequences diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index 87fb4117ac1..a1a93ca19b1 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -4,7 +4,7 @@ process SEQUENZAUTILS_BAM2SEQZ { conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(normalbam), path(tumourbam) diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index c48af9cc868..284c8a4f311 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -4,7 +4,7 @@ process SEQUENZAUTILS_GCWIGGLE { conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 64af395c40e..38c82e1f932 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -5,7 +5,7 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) def container_image = "/seqwish:0.7.6--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index d94c260766e..600218f1e4b 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -4,7 +4,7 @@ process SEROBA_RUN { conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) def container_image = "/seroba:1.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index 7db08d4ac6d..f80c4562ec1 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -4,7 +4,7 @@ process SEXDETERRMINE { conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) def container_image = "/sexdeterrmine:1.1.2--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(depth) diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 6e09ce900fa..4bbb9a729e7 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -4,7 +4,7 @@ process SHASTA { conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) def container_image = "/shasta:0.8.0--h7d875b9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index 80ce221969f..80fdc4bfd56 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -4,7 +4,7 @@ process SHASUM { conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'ubuntu:20.04' }" input: diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index b21aaed75eb..650547fdf64 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -4,7 +4,7 @@ process SHIGATYPER { conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) def container_image = "/shigatyper%3A2.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 9839298c414..cb66f702a0e 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -4,7 +4,7 @@ process SHOVILL { conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) def container_image = "/shovill:1.1.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 9f2e5c5ea33..9d485a5eda6 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -4,7 +4,7 @@ process SISTR { conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) def container_image = "/sistr_cmd:1.1.1--pyh864c0ab_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 19160de8fbe..9eb8de25d6e 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -5,7 +5,7 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) def container_image = "/slimfastq:2.04--h87f3376_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index d4423e66006..2ddafcda8c5 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -4,7 +4,7 @@ process SNAPALIGNER_ALIGN { conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) def container_image = "/snap-aligner:2.0.1--hd03093a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index cd9e63dd7c7..69997b23acf 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -4,7 +4,7 @@ process SNAPALIGNER_INDEX { conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) def container_image = "/snap-aligner:2.0.1--hd03093a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index 033b1236275..0a04679a307 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -4,7 +4,7 @@ process SNIPPY_CORE { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) def container_image = "/snippy:4.6.0--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index a86b8f215f9..d1055362d51 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -4,7 +4,7 @@ process SNIPPY_RUN { conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) def container_image = "/snippy:4.6.0--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 7d2dcb79dd0..7528cf6c432 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -4,7 +4,7 @@ process SNPDISTS { conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) def container_image = "/snp-dists:0.8.2--h5bf99c6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 2eac6019a32..730fb9b3b1f 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -4,7 +4,7 @@ process SNPEFF { conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) def container_image = "/snpeff:5.1--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index 9747d394831..70338bf51e2 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -4,7 +4,7 @@ process SNPSIFT_SPLIT { conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) def container_image = "/snpsift:4.3.1t--hdfd78af_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index a1b3258e2f8..f9c26a0ff20 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -3,7 +3,7 @@ process SNPSITES { conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) def container_image = "/snp-sites:2.5.1--hed695b0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 9663d1e6adb..086f1bb9969 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -5,7 +5,7 @@ process SOMALIER_EXTRACT { conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) def container_image = "/somalier:0.2.15--h37c5b7d_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index 1a5ac8f59db..dcc0a37b5cd 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -5,7 +5,7 @@ process SOMALIER_RELATE { conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) def container_image = "/somalier:0.2.15--h37c5b7d_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(extract) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 3b42d05d8d8..e3da3a8b0ce 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -4,7 +4,7 @@ process SORTMERNA { conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) def container_image = "/sortmerna:4.3.4--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index 7f9643f37a3..26a37ef14f2 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -4,7 +4,7 @@ process SOURMASH_SKETCH { conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) def container_image = "/sourmash:4.2.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 4cb65780033..2b043094781 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -4,7 +4,7 @@ process SPADES { conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) def container_image = "/spades:3.15.4--h95f258a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index 5dbadb31333..f1d4d6c097b 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -4,7 +4,7 @@ process SPATYPER { conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) def container_image = "/spatyper:0.3.3--pyhdfd78af_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index cfa2d728eff..7c86a0cf5a6 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -4,7 +4,7 @@ process SRATOOLS_FASTERQDUMP { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) def container_image = "/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 7a041b188ba..b73ae42af14 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -4,7 +4,7 @@ process SRATOOLS_PREFETCH { conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), val(id) diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 1263d4022a7..10ff4533e33 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -4,7 +4,7 @@ process SRST2_SRST2 { conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) def container_image = "/srst2%3A0.2.0--py27_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 4e445393dea..8ec83c797e1 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -5,7 +5,7 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) def container_image = "/ssuissero%3A1.0.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index 61d9cfa5cd9..5d04aedb85f 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -4,7 +4,7 @@ process STADENIOLIB_SCRAMBLE { conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) def container_image = "/staden_io_lib:1.14.14--h0d9da7e_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index 49c6a1eb6a3..4cf5eb47f5f 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -4,7 +4,7 @@ process STAPHOPIASCCMEC { conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) def container_image = "/staphopia-sccmec:1.0.0--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index a9c9484d1b5..33575afe002 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,7 +4,7 @@ process STAR_ALIGN { conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index a32ad2d1a2c..c0b52157e8b 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -4,7 +4,7 @@ process STAR_GENOMEGENERATE { conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 61be16073fb..5fce33dfec3 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -4,7 +4,7 @@ process STRANGER { conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) def container_image = "/stranger:0.8.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 24e4d4caf7c..245ce5d2ab6 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -4,7 +4,7 @@ process STRELKA_GERMLINE { conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) def container_image = "/strelka:2.9.10--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index a8fae6ff4dc..db73ab1ff4a 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -4,7 +4,7 @@ process STRELKA_SOMATIC { conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) def container_image = "/strelka:2.9.10--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 08a245c635a..92077e1a3bd 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -4,7 +4,7 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) def container_image = "/stringtie:2.2.1--hecb563c_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 22013c2928e..e87e9782cfb 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -4,7 +4,7 @@ process STRINGTIE_STRINGTIE { conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) def container_image = "/stringtie:2.2.1--hecb563c_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 34180fcaa27..747544d0672 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,7 +4,7 @@ process SUBREAD_FEATURECOUNTS { conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) def container_image = "/subread:2.0.1--hed695b0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 2ab7b7d7f10..f12dd0315b2 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -3,7 +3,7 @@ process SVDB_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 8dc5ac01c14..4d8763dd684 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -4,7 +4,7 @@ process SVDB_QUERY { conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) def container_image = "/svdb:2.6.1--py39h5371cbf_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index f45b50e7abc..ae776230e0b 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -4,7 +4,7 @@ process SVTK_STANDARDIZE { conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) def container_image = "/svtk:0.0.20190615--py37h73a75cf_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index efc3884d3f9..5582261a2eb 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,7 +4,7 @@ process TABIX_BGZIPTABIX { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) def container_image = "/tabix:1.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 0a2327f37d9..747d6872e33 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,7 +4,7 @@ process TABIX_TABIX { conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) def container_image = "/tabix:1.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 4a2639fe65b..706006d3bbe 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -4,7 +4,7 @@ process TAILFINDR { conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) def container_image = "/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index 7b6b4972a9a..ae7250f67fe 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -4,7 +4,7 @@ process TBPROFILER_PROFILE { conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) def container_image = "/tb-profiler:3.0.8--pypyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index fc7569a095a..8720e29a339 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -4,7 +4,7 @@ process TIDDIT_COV { conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) def container_image = "/tiddit:3.0.0--py39h59fae87_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index c5646341463..7720552e3e8 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -4,7 +4,7 @@ process TIDDIT_SV { conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) def container_image = "/tiddit:3.1.0--py39h59fae87_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index 18475afe6ac..5570995358d 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -4,7 +4,7 @@ process TRANSDECODER_LONGORF { conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'quay.io/comp-bio-aging/transdecoder' }" input: diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index 2b3b6f429dd..e203893a122 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -4,7 +4,7 @@ process TRANSDECODER_PREDICT { conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } 'quay.io/comp-bio-aging/transdecoder' }" input: diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 1a821563fd4..17e5205e113 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,7 +4,7 @@ process TRIMGALORE { conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) def container_image = "/trim-galore:0.6.7--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index da5d1203d14..c48e1165363 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -4,7 +4,7 @@ process TRIMMOMATIC { conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) def container_image = "/trimmomatic:0.39--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index d94fc793afb..1a92d7de486 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -5,7 +5,7 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) def container_image = "/ucsc-bedclip:377--h0b8a92a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 867200882fc..0e453a43711 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -5,7 +5,7 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) def container_image = "/ucsc-bedgraphtobigwig:377--h446ed27_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index ddb22f54199..d7a398a64c2 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -5,7 +5,7 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) def container_image = "/ucsc-bedtobigbed:377--ha8a8165_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index 48cd17b08ee..d9fa3f32fd7 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -5,7 +5,7 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) def container_image = "/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index c6f37acd3a1..99e795e6014 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -5,7 +5,7 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) def container_image = "/ucsc-liftover:377--h0b8a92a_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 5897831adbe..7148ae9aade 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -5,7 +5,7 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) def container_image = "/ucsc-wigtobigwig:377--h0b8a92a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(wig) diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index 8fa09e07656..2c5e5e3d999 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -4,7 +4,7 @@ process ULTRA_ALIGN { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 33ba2d3525c..4ab4d258713 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -4,7 +4,7 @@ process ULTRA_INDEX { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: path fasta diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index 5f3db8c1fd1..cd187d1313c 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -4,7 +4,7 @@ process ULTRA_PIPELINE { conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 6fa32e49619..c02829893a8 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -4,7 +4,7 @@ process UMITOOLS_DEDUP { conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 67bf2804746..552ed09e66d 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -4,7 +4,7 @@ process UMITOOLS_EXTRACT { conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index 4f4767ef0aa..a78dbec983e 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -4,7 +4,7 @@ process UNICYCLER { conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) def container_image = "/unicycler:0.4.8--py38h8162308_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 88fe0838849..5c66fb57cd5 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,7 +4,7 @@ process UNTAR { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n 'ubuntu:20.04' }" diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index b616f7bb482..915ca337733 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -4,7 +4,7 @@ process UNZIP { conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) def container_image = "/p7zip:15.09--h2d50403_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 940a976318b..43cd571b9ee 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -4,7 +4,7 @@ process VARDICTJAVA { conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) def container_image = "/vardict-java:1.8.3--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 89585f76941..c0bb54bd536 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -5,7 +5,7 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) def container_image = "/variantbam:1.4.4a--h7d7f7ad_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 9f839252dec..176948798e6 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -5,7 +5,7 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) def container_image = "/vcf2db:2020.02.24--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index 4d1d8b1e24b..dddef79f9ac 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -6,7 +6,7 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) def container_image = "/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 6ef6bc7f40e..953c45b72e8 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -4,7 +4,7 @@ process VCFANNO { conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) def container_image = "/vcfanno:0.3.3--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index de179d4af17..bb802f2884f 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -4,7 +4,7 @@ process VCFLIB_VCFBREAKMULTI { conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) def container_image = "/vcflib:1.0.3--hecb563c_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index a199d3a0990..5c8a5fc3ce6 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -5,7 +5,7 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) def container_image = "/vcflib:1.0.3--hecb563c_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index affbf58b251..82be8643bf3 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -4,7 +4,7 @@ process VCFTOOLS { conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) def container_image = "/vcftools:0.1.16--he513fc3_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 2d94bba1615..118064fc94c 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -4,7 +4,7 @@ process VERIFYBAMID_VERIFYBAMID2 { conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) def container_image = "/verifybamid2:2.0.1--hbb20b25_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 82e863fbf7a..1f8fe19cc0f 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -4,7 +4,7 @@ process VSEARCH_SINTAX { conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) def container_image = "/vsearch:2.21.1--h95f258a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index b1d8577afe4..e7eafbb6b1d 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -4,7 +4,7 @@ process VSEARCH_USEARCHGLOBAL { conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) def container_image = "/vsearch:2.21.1--h95f258a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index 6a7dd67e1f1..d022ad10337 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -4,7 +4,7 @@ process WGSIM { conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) def container_image = "/wgsim:1.0--h5bf99c6_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index 522712e4d4c..ab94ee060a8 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -4,7 +4,7 @@ process WHAMG { conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) def container_image = "/wham:1.8.0.1.2017.05.03--h8b12597_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index b5997edc512..b6fe4fc583c 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -4,7 +4,7 @@ process YARA_INDEX { conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) def container_image = "/yara:1.0.2--2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 90af0e7c579..a587abba701 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -4,7 +4,7 @@ process YARA_MAPPER { conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } n input: diff --git a/tests/modules/nf-core/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config index 5affc412fa4..6d1f18bcdf5 100644 --- a/tests/modules/nf-core/vcf2maf/nextflow.config +++ b/tests/modules/nf-core/vcf2maf/nextflow.config @@ -6,7 +6,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: 'test_vcf2maf_no_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" - container = ${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2maf:1.6.21--hdfd78af_0 + container = ${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2maf:1.6.21--hdfd78af_0 } withName: 'test_vcf2maf_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species}" From 794867cb2ea1f70bb4f99eece5fc3f1ee533b6d7 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 13 Oct 2022 18:54:00 +0200 Subject: [PATCH 19/21] fix: Remove bad edits --- modules/nf-core/abricate/run/main.nf | 2 +- modules/nf-core/abricate/summary/main.nf | 2 +- modules/nf-core/amps/main.nf | 1 - modules/nf-core/amrfinderplus/update/main.nf | 1 - modules/nf-core/antismash/antismashlite/main.nf | 2 ++ .../antismash/antismashlitedownloaddatabases/main.nf | 6 ++++-- modules/nf-core/ariba/getref/main.nf | 1 - modules/nf-core/ariba/run/main.nf | 1 - modules/nf-core/arriba/main.nf | 1 - modules/nf-core/artic/guppyplex/main.nf | 1 - modules/nf-core/biobambam/bammarkduplicates2/main.nf | 2 ++ modules/nf-core/biobambam/bamsormadup/main.nf | 2 ++ modules/nf-core/biscuit/vcf2bed/main.nf | 1 - modules/nf-core/bowtie2/align/main.nf | 3 ++- modules/nf-core/busco/main.nf | 1 - modules/nf-core/bwa/index/main.nf | 1 - modules/nf-core/bwa/mem/main.nf | 1 - modules/nf-core/bwa/sampe/main.nf | 1 - modules/nf-core/bwamem2/index/main.nf | 1 - modules/nf-core/bwamem2/mem/main.nf | 1 - modules/nf-core/cat/fastq/main.nf | 3 +-- modules/nf-core/clonalframeml/main.nf | 1 - modules/nf-core/dastool/dastool/main.nf | 1 - modules/nf-core/dastool/fastatocontig2bin/main.nf | 1 - modules/nf-core/dastool/scaffolds2bin/main.nf | 1 - modules/nf-core/deeparg/downloaddata/main.nf | 1 + modules/nf-core/deeparg/predict/main.nf | 1 + modules/nf-core/deeptools/bamcoverage/main.nf | 1 - modules/nf-core/deeptools/computematrix/main.nf | 1 - modules/nf-core/deeptools/plotfingerprint/main.nf | 1 - modules/nf-core/deeptools/plotheatmap/main.nf | 1 - modules/nf-core/deeptools/plotprofile/main.nf | 1 - modules/nf-core/dragonflye/main.nf | 1 - modules/nf-core/dshbio/exportsegments/main.nf | 1 - modules/nf-core/dshbio/filterbed/main.nf | 1 - modules/nf-core/dshbio/filtergff3/main.nf | 1 - modules/nf-core/dshbio/splitbed/main.nf | 1 - modules/nf-core/dshbio/splitgff3/main.nf | 1 - modules/nf-core/eido/convert/main.nf | 2 ++ modules/nf-core/eido/validate/main.nf | 2 ++ modules/nf-core/elprep/filter/main.nf | 1 - modules/nf-core/endorspy/main.nf | 1 - modules/nf-core/entrezdirect/xtract/main.nf | 2 +- modules/nf-core/faqcs/main.nf | 2 +- modules/nf-core/fastawindows/main.nf | 1 - modules/nf-core/fastp/main.nf | 1 - modules/nf-core/fasttree/main.nf | 1 - modules/nf-core/fcs/fcsadaptor/main.nf | 2 ++ modules/nf-core/ffq/main.nf | 1 - modules/nf-core/flye/main.nf | 1 - modules/nf-core/fq/lint/main.nf | 3 ++- modules/nf-core/gamma/gamma/main.nf | 2 +- modules/nf-core/gappa/examineassign/main.nf | 1 - modules/nf-core/gappa/examinegraft/main.nf | 1 - modules/nf-core/gappa/examineheattree/main.nf | 1 - modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 1 - modules/nf-core/gatk4/filtermutectcalls/main.nf | 3 ++- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 1 - modules/nf-core/gatk4/genotypegvcfs/main.nf | 1 - modules/nf-core/gatk4/selectvariants/main.nf | 1 - modules/nf-core/genmod/annotate/main.nf | 1 - modules/nf-core/genmod/compound/main.nf | 1 - modules/nf-core/genmod/models/main.nf | 1 - modules/nf-core/genmod/score/main.nf | 1 - modules/nf-core/genotyphi/parse/main.nf | 1 - modules/nf-core/gffread/main.nf | 1 - modules/nf-core/gubbins/main.nf | 1 - modules/nf-core/gunzip/main.nf | 3 +-- modules/nf-core/haplogrep2/classify/main.nf | 1 - modules/nf-core/happy/happy/main.nf | 1 - modules/nf-core/hisat2/align/main.nf | 1 - modules/nf-core/hmmer/eslreformat/main.nf | 1 - modules/nf-core/hmmer/hmmsearch/main.nf | 1 - modules/nf-core/homer/annotatepeaks/main.nf | 1 - modules/nf-core/homer/findpeaks/main.nf | 1 - modules/nf-core/homer/maketagdirectory/main.nf | 1 - modules/nf-core/homer/makeucscfile/main.nf | 1 - modules/nf-core/homer/pos2bed/main.nf | 1 - modules/nf-core/hpsuissero/main.nf | 2 +- modules/nf-core/imputeme/vcftoprs/main.nf | 6 +++++- modules/nf-core/krakentools/combinekreports/main.nf | 1 - modules/nf-core/last/dotplot/main.nf | 1 - modules/nf-core/last/lastdb/main.nf | 1 - modules/nf-core/last/postmask/main.nf | 1 - modules/nf-core/last/split/main.nf | 1 - modules/nf-core/legsta/main.nf | 2 +- modules/nf-core/lissero/main.nf | 1 - modules/nf-core/manta/convertinversion/main.nf | 1 - modules/nf-core/manta/germline/main.nf | 1 - modules/nf-core/manta/somatic/main.nf | 1 - modules/nf-core/manta/tumoronly/main.nf | 1 - modules/nf-core/mashtree/main.nf | 1 - modules/nf-core/maxquant/lfq/main.nf | 6 +++--- modules/nf-core/mcroni/main.nf | 2 +- modules/nf-core/md5sum/main.nf | 3 +-- modules/nf-core/meningotype/main.nf | 1 - modules/nf-core/mlst/main.nf | 1 - modules/nf-core/mobsuite/recon/main.nf | 2 +- modules/nf-core/mtnucratio/main.nf | 1 - modules/nf-core/multiqc/main.nf | 1 - modules/nf-core/multivcfanalyzer/main.nf | 1 - modules/nf-core/nanolyse/main.nf | 1 - modules/nf-core/nextgenmap/main.nf | 2 +- modules/nf-core/pairtools/flip/main.nf | 1 - modules/nf-core/pangolin/main.nf | 1 - modules/nf-core/paraclu/main.nf | 1 - modules/nf-core/pasty/main.nf | 1 - modules/nf-core/phyloflash/main.nf | 1 - modules/nf-core/prodigal/main.nf | 1 - modules/nf-core/prokka/main.nf | 2 +- modules/nf-core/rapidnj/main.nf | 1 - modules/nf-core/rhocall/annotate/main.nf | 1 - modules/nf-core/scoary/main.nf | 1 - modules/nf-core/shasum/main.nf | 3 +-- modules/nf-core/shigatyper/main.nf | 2 +- modules/nf-core/sistr/main.nf | 1 - modules/nf-core/snpsift/split/main.nf | 1 - modules/nf-core/snpsites/main.nf | 1 - modules/nf-core/srst2/srst2/main.nf | 2 +- modules/nf-core/ssuissero/main.nf | 2 +- modules/nf-core/staphopiasccmec/main.nf | 1 - modules/nf-core/stringtie/stringtie/main.nf | 1 - modules/nf-core/subread/featurecounts/main.nf | 1 - modules/nf-core/tabix/bgzip/main.nf | 3 ++- modules/nf-core/transdecoder/longorf/main.nf | 5 ++--- modules/nf-core/transdecoder/predict/main.nf | 3 +-- modules/nf-core/trimgalore/main.nf | 1 - modules/nf-core/untar/main.nf | 4 +--- modules/nf-core/unzip/main.nf | 1 - modules/nf-core/vcfanno/main.nf | 1 - modules/nf-core/yara/index/main.nf | 1 - modules/nf-core/yara/mapper/main.nf | 1 - tests/modules/nf-core/vcf2maf/nextflow.config | 2 +- 133 files changed, 57 insertions(+), 137 deletions(-) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index feb389602ed..a86716affce 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -3,7 +3,7 @@ process ABRICATE_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - def container_image = "/abricate%3A1.0.1--ha8f3691_1" + def container_image = "/abricate:1.0.1--ha8f3691_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index c1e1c5f634b..76fa5fd51dc 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -3,7 +3,7 @@ process ABRICATE_SUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - def container_image = "/abricate%3A1.0.1--ha8f3691_1" + def container_image = "/abricate:1.0.1--ha8f3691_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index a50b4eb9464..ee27f3f3dd1 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -4,7 +4,6 @@ process AMPS { conda (params.enable_conda ? "bioconda::hops=0.35" : null) def container_image = "/hops:0.35--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index e60ee7d62a3..72c6b316c1c 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -5,7 +5,6 @@ process AMRFINDERPLUS_UPDATE { conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 8f6f157c447..1f386692b83 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -7,7 +7,9 @@ process ANTISMASH_ANTISMASHLITE { container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } containerOptions { + workflow.containerEngine == 'singularity' ? "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : + workflow.containerEngine == 'docker' ? "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : '' } diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index c62d9e0e4ad..5185eb42175 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -12,8 +12,10 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { */ containerOptions { - "-B $database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css,$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection,$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" : - "-v \$PWD/$database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css -v \$PWD/$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection -v \$PWD/$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" : + workflow.containerEngine == 'singularity' ? + "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : + workflow.containerEngine == 'docker' ? + "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : '' } diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index 4ba19dd2fc0..38b50930cc3 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -5,7 +5,6 @@ process ARIBA_GETREF { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) def container_image = "/ariba:2.14.6--py39h67e14b5_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 351daa2e950..0fd602ff8fb 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -5,7 +5,6 @@ process ARIBA_RUN { conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) def container_image = "/ariba:2.14.6--py39h67e14b5_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 7cf484e057c..49d0f6ebb1a 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -5,7 +5,6 @@ process ARRIBA { conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) def container_image = "/arriba:2.3.0--haa8aa89_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 76f94bf78a7..b7103f212bb 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -5,7 +5,6 @@ process ARTIC_GUPPYPLEX { conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) def container_image = "/artic:1.2.2--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/modules/nf-core/biobambam/bammarkduplicates2/main.nf index 2a5fb811ee5..a72be6a2242 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -3,6 +3,8 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 { label 'process_medium' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) + def container_image = "/biobambam:2.0.183--h9f5acd7_1" + container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index 56f55d8893b..1073da0ba3e 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -3,6 +3,8 @@ process BIOBAMBAM_BAMSORMADUP { label "process_medium" conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) + def container_image = "/biobambam:2.0.183--h9f5acd7_1" + container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) input: tuple val(meta), path(bams, stageAs: "?/*") diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index 26d5570bfcd..af7fc7d6db0 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -5,7 +5,6 @@ process BISCUIT_VCF2BED { conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index fa8d2d202d9..be80dbdba95 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -3,7 +3,8 @@ process BOWTIE2_ALIGN { label "process_high" conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) - "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" : + def container_image = "/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" + container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) input: tuple val(meta), path(reads) diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 35a1927b548..dad9c36d1bd 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -5,7 +5,6 @@ process BUSCO { conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) def container_image = "/busco:5.4.3--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index bd7a00e6901..b588cd4859b 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -5,7 +5,6 @@ process BWA_INDEX { conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) def container_image = "/bwa:0.7.17--hed695b0_7" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index c82a8000df2..9cf25e101da 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -5,7 +5,6 @@ process BWA_MEM { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 690e5e7d748..f882d945c86 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -5,7 +5,6 @@ process BWA_SAMPE { conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 0e60cf630e6..9b142ff3cd4 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -5,7 +5,6 @@ process BWAMEM2_INDEX { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) def container_image = "/bwa-mem2:2.2.1--he513fc3_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index f61f28d86e4..6f9e93d98eb 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -5,7 +5,6 @@ process BWAMEM2_MEM { conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 113dca719df..016c8a61fb7 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -4,8 +4,7 @@ process CAT_FASTQ { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } - 'ubuntu:20.04' }" + container { (params.container_registry ?: '' + container_image) } input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 22e207008c4..38508c003dd 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -5,7 +5,6 @@ process CLONALFRAMEML { conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) def container_image = "/clonalframeml:1.12--h7d875b9_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index 721fe5d304a..48a3f5b8d57 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -5,7 +5,6 @@ process DASTOOL_DASTOOL { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) def container_image = "/das_tool:1.1.4--r41hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index 7e8f32092fa..0f2c819c71d 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -5,7 +5,6 @@ process DASTOOL_FASTATOCONTIG2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) def container_image = "/das_tool:1.1.4--r41hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index bf218d16416..d1697b9f1d6 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -5,7 +5,6 @@ process DASTOOL_SCAFFOLDS2BIN { conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) def container_image = "/das_tool:1.1.3--r41hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index d51861acb53..ee8953b2597 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -8,6 +8,7 @@ process DEEPARG_DOWNLOADDATA { We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ + containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } input: diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 3bef899fe4e..135d75014c5 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -9,6 +9,7 @@ process DEEPARG_PREDICT { We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ + containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } input: tuple val(meta), path(fasta), val(model) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 48e73850af7..8f8a2a703ec 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -5,7 +5,6 @@ process DEEPTOOLS_BAMCOVERAGE { conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index e98e69fc4c0..90175ee126e 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -5,7 +5,6 @@ process DEEPTOOLS_COMPUTEMATRIX { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index 8985e3c8dda..98b65ee43ac 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -5,7 +5,6 @@ process DEEPTOOLS_PLOTFINGERPRINT { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index bdf1c6c7bb3..c612b271ef3 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -5,7 +5,6 @@ process DEEPTOOLS_PLOTHEATMAP { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index 14c1c332805..c3454dc913f 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -5,7 +5,6 @@ process DEEPTOOLS_PLOTPROFILE { conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) def container_image = "/deeptools:3.5.1--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index 6ac9142081e..af6c96cc7bc 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -5,7 +5,6 @@ process DRAGONFLYE { conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) def container_image = "/dragonflye:1.0.11--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 23c36bd5460..982cdbcc254 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -5,7 +5,6 @@ process DSHBIO_EXPORTSEGMENTS { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 526f1cfea6e..f7e4ca41cf6 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -5,7 +5,6 @@ process DSHBIO_FILTERBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index ba2cfe102c4..c12b652153d 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -5,7 +5,6 @@ process DSHBIO_FILTERGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index bd3d319cd02..8f737061a93 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -5,7 +5,6 @@ process DSHBIO_SPLITBED { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 619ab53e175..9e87d5fddf2 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -5,7 +5,6 @@ process DSHBIO_SPLITGFF3 { conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) def container_image = "/dsh-bio:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/eido/convert/main.nf b/modules/nf-core/eido/convert/main.nf index 1bc7db167d5..48f27bedabe 100644 --- a/modules/nf-core/eido/convert/main.nf +++ b/modules/nf-core/eido/convert/main.nf @@ -3,6 +3,8 @@ process EIDO_CONVERT { label 'process_single' conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null) + // FIXME https://github.com/nf-core/modules/pull/2291 + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' : 'biocontainers/eido:0.1.9_cv1' }" diff --git a/modules/nf-core/eido/validate/main.nf b/modules/nf-core/eido/validate/main.nf index b6c8a40d6b8..bd6f860b579 100644 --- a/modules/nf-core/eido/validate/main.nf +++ b/modules/nf-core/eido/validate/main.nf @@ -3,6 +3,8 @@ process EIDO_VALIDATE { label 'process_single' conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null) + // FIXME https://github.com/nf-core/modules/pull/2291 + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' : 'biocontainers/eido:0.1.9_cv2' }" diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 1865efd5e57..91ab2e0bc92 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -5,7 +5,6 @@ process ELPREP_FILTER { conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) def container_image = "/elprep:5.1.2--he881be0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index b3340c7e0b3..ad60dc6e453 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -5,7 +5,6 @@ process ENDORSPY { conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) def container_image = "/endorspy:0.4--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index d83daadef91..b7d0d66179f 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -3,7 +3,7 @@ process ENTREZDIRECT_XTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) -def container_image = "/entrez-direct:16.2--he881be0_1" + def container_image = "/entrez-direct:16.2--he881be0_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index 472792c1592..19b7d34caf7 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -3,7 +3,7 @@ process FAQCS { label 'process_medium' conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) - def container_image = "/faqcs%3A2.10--r41h9a82719_2" + def container_image = "/faqcs:2.10--r41h9a82719_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index 24c9f42cbce..aea224e36ae 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -5,7 +5,6 @@ process FASTAWINDOWS { conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) def container_image = "/fasta_windows:0.2.4--hec16e2b_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index fb1b5d0f862..3cd666089e2 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -5,7 +5,6 @@ process FASTP { conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) def container_image = "/fastp:0.23.2--h79da9fb_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index a6aab2f1823..85d5d224bbd 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -4,7 +4,6 @@ process FASTTREE { conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) def container_image = "/fasttree:2.1.10--h516909a_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path alignment diff --git a/modules/nf-core/fcs/fcsadaptor/main.nf b/modules/nf-core/fcs/fcsadaptor/main.nf index 772341f0687..a230624cf9c 100644 --- a/modules/nf-core/fcs/fcsadaptor/main.nf +++ b/modules/nf-core/fcs/fcsadaptor/main.nf @@ -6,6 +6,8 @@ process FCS_FCSADAPTOR { exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers." } // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + // FIXME https://github.com/nf-core/modules/pull/2291 + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif': 'ncbi/fcs-adaptor:0.2.3' }" diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 9a2a648aca9..476eb2efa57 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -5,7 +5,6 @@ process FFQ { conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) def container_image = "/ffq:0.2.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: val ids diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index c1e177ef033..6af34bb0bbe 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -5,7 +5,6 @@ process FLYE { conda (params.enable_conda ? "bioconda::flye=2.9" : null) def container_image = "/flye:2.9--py39h6935b12_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index f7516dadf4d..a4902639366 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -3,7 +3,8 @@ process FQ_LINT { label 'process_low' conda (params.enable_conda ? "bioconda::fq=0.9.1" : null) - 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': + def container_image = "/fq:0.9.1--h9ee0642_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 0f759462f23..00b03593f1c 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -5,7 +5,7 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) - def container_image = "/gamma%3A2.1--hdfd78af_0" + def container_image = "/gamma:2.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 744c2b80b1b..6e2a928f008 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -5,7 +5,6 @@ process GAPPA_EXAMINEASSIGN { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) def container_image = "/gappa:0.8.0--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 2540110305c..2d1feebbd21 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -5,7 +5,6 @@ process GAPPA_EXAMINEGRAFT { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) def container_image = "/gappa:0.8.0--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index c4ac834e28d..bca658226d7 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -5,7 +5,6 @@ process GAPPA_EXAMINEHEATTREE { conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) def container_image = "/gappa:0.8.0--h9a82719_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index aaede205c5d..17c1a4a229d 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -5,7 +5,6 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 7bad97d53a9..54c95056047 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -3,7 +3,8 @@ process GATK4_FILTERMUTECTCALLS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + def container_image = "/gatk4:4.2.6.1--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index edc9593532d..f7cd4fdd712 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -5,7 +5,6 @@ process GATK4_GATHERBQSRREPORTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 7966cf5d391..8172c9c911c 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -5,7 +5,6 @@ process GATK4_GENOTYPEGVCFS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 09147f2da2c..a831f3bc52a 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -5,7 +5,6 @@ process GATK4_SELECTVARIANTS { conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) def container_image = "/gatk4:4.2.6.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index f99f35b8596..fb978ffdc97 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -5,7 +5,6 @@ process GENMOD_ANNOTATE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 6bd55a0d208..936ad0eb567 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -5,7 +5,6 @@ process GENMOD_COMPOUND { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 3803e81a429..900fbc99349 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -5,7 +5,6 @@ process GENMOD_MODELS { conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 0fa66dfb7dd..3c11dab9eac 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -5,7 +5,6 @@ process GENMOD_SCORE { conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) def container_image = "/genmod:3.7.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index 2cfc25c0923..d1ae2ab6d89 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -5,7 +5,6 @@ process GENOTYPHI_PARSE { conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) def container_image = "/genotyphi:1.9.1--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(json) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index a424fb2faa7..a81ac4e90ee 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -5,7 +5,6 @@ process GFFREAD { conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) def container_image = "/gffread:0.12.1--h8b12597_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path gff diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index f26603cf300..9de061c768b 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -4,7 +4,6 @@ process GUBBINS { conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) def container_image = "/gubbins:3.0.0--py39h5bf99c6_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path alignment diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 5542a071317..e8e440e1508 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -4,8 +4,7 @@ process GUNZIP { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } - 'ubuntu:20.04' }" + container { (params.container_registry ?: '' + container_image) } input: tuple val(meta), path(archive) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 137c84e9990..019aa317794 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -5,7 +5,6 @@ process HAPLOGREP2_CLASSIFY { conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) def container_image = "/haplogrep:2.4.0--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index 66960c60d6d..cba1118ed3e 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -6,7 +6,6 @@ process HAPPY_HAPPY { conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 32128fd0f71..3979b1de579 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -6,7 +6,6 @@ process HISAT2_ALIGN { conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 93d30d16e72..9a24fee96c1 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -5,7 +5,6 @@ process HMMER_ESLREFORMAT { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index d60a2986a7e..3a7b2d4461f 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -5,7 +5,6 @@ process HMMER_HMMSEARCH { conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) def container_image = "/hmmer:3.3.2--h1b792b2_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index e680036e6e3..185a27f1903 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -6,7 +6,6 @@ process HOMER_ANNOTATEPEAKS { conda (params.enable_conda ? "bioconda::homer=4.11" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 257582505d1..7c5dcae4aba 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -6,7 +6,6 @@ process HOMER_FINDPEAKS { conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 85836267a61..9cce134da4f 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -7,7 +7,6 @@ process HOMER_MAKETAGDIRECTORY { conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) def container_image = "/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 9e955846a24..579377a3920 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -6,7 +6,6 @@ process HOMER_MAKEUCSCFILE { conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index 5da6aa425e9..3bbc1f480f4 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -6,7 +6,6 @@ process HOMER_POS2BED { conda (params.enable_conda ? "bioconda::homer=4.11" : null) def container_image = "/homer:4.11--pl526hc9558a2_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 17b3ee86586..787d938cbab 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -4,7 +4,7 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) - def container_image = "/hpsuissero%3A1.0.1--hdfd78af_0" + def container_image = "/hpsuissero:1.0.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/imputeme/vcftoprs/main.nf b/modules/nf-core/imputeme/vcftoprs/main.nf index fc8c6ef6c73..b3e03ec7767 100644 --- a/modules/nf-core/imputeme/vcftoprs/main.nf +++ b/modules/nf-core/imputeme/vcftoprs/main.nf @@ -2,7 +2,11 @@ process IMPUTEME_VCFTOPRS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "YOUR-TOOL-HERE" : null) + if (params.enable_conda) { + exit 1, "Conda environments cannot be used when using bases2fastq. Please use docker or singularity containers." + } + // FIXME https://github.com/nf-core/modules/pull/2291 + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img' : 'biocontainers/imputeme:vv1.0.7_cv1' }" diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index 47f8f363ce6..bfc5da814a5 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -4,7 +4,6 @@ process KRAKENTOOLS_COMBINEKREPORTS { conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) def container_image = "/krakentools:1.2--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index e6b5abb00ef..5bd9faa068b 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -5,7 +5,6 @@ process LAST_DOTPLOT { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index c50b91e70c7..f710b02e700 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -5,7 +5,6 @@ process LAST_LASTDB { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 93a6f8d64a6..2fdcecee821 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -5,7 +5,6 @@ process LAST_POSTMASK { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 058a225c0da..2106f2afe4b 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -5,7 +5,6 @@ process LAST_SPLIT { conda (params.enable_conda ? 'bioconda::last=1250' : null) def container_image = "/last:1250--h2e03b76_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(maf) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index d6e2a8ea918..d5987b1a9d3 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -3,7 +3,7 @@ process LEGSTA { label 'process_medium' conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) - def container_image = "/legsta%3A0.5.1--hdfd78af_2" + def container_image = "/legsta:0.5.1--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index 3a906448391..f8f25ed8de4 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -5,7 +5,6 @@ process LISSERO { conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) def container_image = "/lissero:0.4.9--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 8397f96dee2..0c30d771f1d 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -5,7 +5,6 @@ process MANTA_CONVERTINVERSION { conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 9aea35649d1..b22fcb97c33 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -5,7 +5,6 @@ process MANTA_GERMLINE { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) def container_image = "/manta:1.6.0--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index 9fc249e535f..bbd00d11600 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -5,7 +5,6 @@ process MANTA_SOMATIC { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) def container_image = "/manta:1.6.0--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index e6790a9f14c..47cf68df3e1 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -5,7 +5,6 @@ process MANTA_TUMORONLY { conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) def container_image = "/manta:1.6.0--h9ee0642_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index f22bfa7390f..4ddb9f23e05 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -5,7 +5,6 @@ process MASHTREE { conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) def container_image = "/mashtree:1.2.0--pl526h516909a_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index 55e603f79b1..f0a8592a03b 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -1,10 +1,10 @@ process MAXQUANT_LFQ { tag "$meta.id" label 'process_long' + conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null) - container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" - } else { - } + def container_image = "/maxquant:2.0.3.0--py310hdfd78af_1" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(fasta), path(paramfile) diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index 224ae3ec9c1..aa36e56a765 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -4,7 +4,7 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) - def container_image = "/mcroni%3A1.0.4--pyh5e36f6f_0" + def container_image = "/mcroni:1.0.4--pyh5e36f6f_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index 5471b2ba310..0f95fb8fbd8 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -4,8 +4,7 @@ process MD5SUM { conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } - 'ubuntu:20.04' }" + container { (params.container_registry ?: '' + container_image) } input: tuple val(meta), path(file) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index c86c107c278..75d81ff2406 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -5,7 +5,6 @@ process MENINGOTYPE { conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) def container_image = "/meningotype:0.8.5--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 2d1ee12b85a..0d728c4a750 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -5,7 +5,6 @@ process MLST { conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) def container_image = "/mlst:2.19.0--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index f2c88f29381..051889f006d 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -3,7 +3,7 @@ process MOBSUITE_RECON { label 'process_medium' conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) - def container_image = "/mob_suite%3A3.0.3--pyhdfd78af_0" + def container_image = "/mob_suite:3.0.3--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index 7d854012c8c..9ed6a7e42b5 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -5,7 +5,6 @@ process MTNUCRATIO { conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) def container_image = "/mtnucratio:0.7--hdfd78af_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 74a559a448d..7dd8515874c 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,7 +4,6 @@ process MULTIQC { conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) def container_image = "/multiqc:1.13--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 78bca1a5b77..648947ce10a 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -5,7 +5,6 @@ process MULTIVCFANALYZER { conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) def container_image = "/multivcfanalyzer:0.85.2--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path vcfs diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 3626e3c2e61..9045fc60be9 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -5,7 +5,6 @@ process NANOLYSE { conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) def container_image = "/nanolyse:1.2.0--py_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index c4ed5755d4d..50ff5164c1a 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -3,7 +3,7 @@ process NEXTGENMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) - def container_image = "/nextgenmap%3A0.5.5--hc9558a2_4" + def container_image = "/nextgenmap:0.5.5--hc9558a2_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index a717e281b52..1b686db3c9d 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -5,7 +5,6 @@ process PAIRTOOLS_FLIP { conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 7e4fc5baeb8..7f92744ba16 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -5,7 +5,6 @@ process PANGOLIN { conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) def container_image = "/pangolin:4.1.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index 8a6a7485f90..ad1161e55a4 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -6,7 +6,6 @@ process PARACLU { conda (params.enable_conda ? "bioconda::paraclu=10" : null) def container_image = "/paraclu:10--h9a82719_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 09f1b2873e2..d2fb8736b58 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -5,7 +5,6 @@ process PASTY { conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) def container_image = "/pasty:1.0.0--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index 630991f8414..ccc9b62d3fe 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -5,7 +5,6 @@ process PHYLOFLASH { conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) def container_image = "/phyloflash:3.4--hdfd78af_1" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 3c6b9c9504f..0ce6cd3b8f5 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -5,7 +5,6 @@ process PRODIGAL { conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) def container_image = "/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index eebc73ab336..d0624957928 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -3,7 +3,7 @@ process PROKKA { label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) - def container_image = "/prokka%3A1.14.6--pl5321hdfd78af_4" + def container_image = "/prokka:1.14.6--pl5321hdfd78af_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index a7662a2f85d..b03045aac59 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -5,7 +5,6 @@ process RAPIDNJ { conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) def container_image = "/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path alignment diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index c516292d4b8..76f71718a41 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -5,7 +5,6 @@ process RHOCALL_ANNOTATE { conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) def container_image = "/rhocall:0.5.1--py39hbf8eff0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index b546a108088..9ec2a767f29 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -5,7 +5,6 @@ process SCOARY { conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) def container_image = "/scoary:1.6.16--py_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index 80fdc4bfd56..58510c76a07 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -4,8 +4,7 @@ process SHASUM { conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } - 'ubuntu:20.04' }" + container { (params.container_registry ?: '' + container_image) } input: tuple val(meta), path(file) diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index 650547fdf64..aa94cd77a66 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -3,7 +3,7 @@ process SHIGATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) - def container_image = "/shigatyper%3A2.0.1--pyhdfd78af_0" + def container_image = "/shigatyper:2.0.1--pyhdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 9d485a5eda6..84d856b3001 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -5,7 +5,6 @@ process SISTR { conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) def container_image = "/sistr_cmd:1.1.1--pyh864c0ab_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index 70338bf51e2..ab1b1125190 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -5,7 +5,6 @@ process SNPSIFT_SPLIT { conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) def container_image = "/snpsift:4.3.1t--hdfd78af_3" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index f9c26a0ff20..905da8b0fc3 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -4,7 +4,6 @@ process SNPSITES { conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) def container_image = "/snp-sites:2.5.1--hed695b0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: path alignment diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 10ff4533e33..154f1579c8a 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -3,7 +3,7 @@ process SRST2_SRST2 { label 'process_low' conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) - def container_image = "/srst2%3A0.2.0--py27_2" + def container_image = "/srst2:0.2.0--py27_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index 8ec83c797e1..c0c9c38f504 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -4,7 +4,7 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) - def container_image = "/ssuissero%3A1.0.1--hdfd78af_0" + def container_image = "ssuissero:1.0.1--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index 4cf5eb47f5f..c5fd2fd028b 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -5,7 +5,6 @@ process STAPHOPIASCCMEC { conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) def container_image = "/staphopia-sccmec:1.0.0--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index e87e9782cfb..c06a17adea9 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -5,7 +5,6 @@ process STRINGTIE_STRINGTIE { conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) def container_image = "/stringtie:2.2.1--hecb563c_2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 747544d0672..c402b8f33fb 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -5,7 +5,6 @@ process SUBREAD_FEATURECOUNTS { conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) def container_image = "/subread:2.0.1--hed695b0_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 2b79cc28e24..2e0eeb697f6 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -3,7 +3,8 @@ process TABIX_BGZIP { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : + def container_image = "/tabix:1.11--hdfd78af_0" + container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } input: tuple val(meta), path(input) diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index 5570995358d..3d0bcbf92d6 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -3,9 +3,8 @@ process TRANSDECODER_LONGORF { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) -def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } - 'quay.io/comp-bio-aging/transdecoder' }" + def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" + container { (params.container_registry ?: 'quay.io/comp-bio-aging' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index e203893a122..42833f5e269 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -4,8 +4,7 @@ process TRANSDECODER_PREDICT { conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } - 'quay.io/comp-bio-aging/transdecoder' }" + container { (params.container_registry ?: 'quay.io/comp-bio-aging' + container_image) } input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 17e5205e113..1dc9f353eaf 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -5,7 +5,6 @@ process TRIMGALORE { conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) def container_image = "/trim-galore:0.6.7--hdfd78af_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 5c66fb57cd5..7a2bb197c64 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,9 +4,7 @@ process UNTAR { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n - 'ubuntu:20.04' }" + container { (params.container_registry ?: '' + container_image) } input: tuple val(meta), path(archive) diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 915ca337733..6771513823c 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -5,7 +5,6 @@ process UNZIP { conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) def container_image = "/p7zip:15.09--h2d50403_4" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 953c45b72e8..cfd8a012f0a 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -5,7 +5,6 @@ process VCFANNO { conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) def container_image = "/vcfanno:0.3.3--h9ee0642_0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index b6fe4fc583c..cf1750056ab 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -5,7 +5,6 @@ process YARA_INDEX { conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) def container_image = "/yara:1.0.2--2" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index a587abba701..4e57137ef7b 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -5,7 +5,6 @@ process YARA_MAPPER { conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) def container_image = "/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } -n input: tuple val(meta), path(reads) diff --git a/tests/modules/nf-core/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config index 6d1f18bcdf5..0903de1baa7 100644 --- a/tests/modules/nf-core/vcf2maf/nextflow.config +++ b/tests/modules/nf-core/vcf2maf/nextflow.config @@ -6,7 +6,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: 'test_vcf2maf_no_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" - container = ${params.docker_registry ?: 'quay.io/biocontainers'}/vcf2maf:1.6.21--hdfd78af_0 + container = "quay.io/biocontainers/vcf2maf:1.6.21--hdfd78af_0" } withName: 'test_vcf2maf_vep:VCF2MAF' { ext.args = "--ncbi-build ${params.build} --species ${params.species}" From 32eb7c6a361deef2c4ca2e1a9b979b7b6417a7c4 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sat, 15 Oct 2022 18:10:23 -0500 Subject: [PATCH 20/21] refactor: Use join to make images easier to update Co-authored-by: mahesh-panchal --- modules/nf-core/abacas/main.nf | 5 +++-- modules/nf-core/abricate/run/main.nf | 5 +++-- modules/nf-core/abricate/summary/main.nf | 5 +++-- modules/nf-core/adapterremoval/main.nf | 5 +++-- modules/nf-core/adapterremovalfixprefix/main.nf | 5 +++-- modules/nf-core/agrvate/main.nf | 5 +++-- modules/nf-core/allelecounter/main.nf | 5 +++-- modules/nf-core/ampir/main.nf | 5 +++-- modules/nf-core/amplify/predict/main.nf | 5 +++-- modules/nf-core/amps/main.nf | 5 +++-- modules/nf-core/amrfinderplus/run/main.nf | 5 +++-- modules/nf-core/amrfinderplus/update/main.nf | 5 +++-- modules/nf-core/angsd/docounts/main.nf | 5 +++-- modules/nf-core/antismash/antismashlite/main.nf | 5 +++-- .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 5 +++-- modules/nf-core/aria2/main.nf | 5 +++-- modules/nf-core/ariba/getref/main.nf | 5 +++-- modules/nf-core/ariba/run/main.nf | 5 +++-- modules/nf-core/arriba/main.nf | 5 +++-- modules/nf-core/artic/guppyplex/main.nf | 5 +++-- modules/nf-core/artic/minion/main.nf | 5 +++-- modules/nf-core/ascat/main.nf | 5 +++-- modules/nf-core/assemblyscan/main.nf | 5 +++-- modules/nf-core/ataqv/ataqv/main.nf | 5 +++-- modules/nf-core/ataqv/mkarv/main.nf | 5 +++-- modules/nf-core/atlas/call/main.nf | 5 +++-- modules/nf-core/atlas/pmd/main.nf | 5 +++-- modules/nf-core/atlas/recal/main.nf | 5 +++-- modules/nf-core/atlas/splitmerge/main.nf | 5 +++-- modules/nf-core/bakta/main.nf | 5 +++-- modules/nf-core/bamaligncleaner/main.nf | 5 +++-- modules/nf-core/bamcmp/main.nf | 5 +++-- modules/nf-core/bamtools/convert/main.nf | 5 +++-- modules/nf-core/bamtools/split/main.nf | 5 +++-- modules/nf-core/bamtools/stats/main.nf | 5 +++-- modules/nf-core/bamutil/trimbam/main.nf | 5 +++-- modules/nf-core/bandage/image/main.nf | 5 +++-- modules/nf-core/bbmap/align/main.nf | 5 +++-- modules/nf-core/bbmap/bbduk/main.nf | 5 +++-- modules/nf-core/bbmap/bbsplit/main.nf | 5 +++-- modules/nf-core/bbmap/clumpify/main.nf | 5 +++-- modules/nf-core/bbmap/index/main.nf | 5 +++-- modules/nf-core/bbmap/pileup/main.nf | 5 +++-- modules/nf-core/bcftools/annotate/main.nf | 5 +++-- modules/nf-core/bcftools/concat/main.nf | 5 +++-- modules/nf-core/bcftools/consensus/main.nf | 5 +++-- modules/nf-core/bcftools/convert/main.nf | 5 +++-- modules/nf-core/bcftools/filter/main.nf | 5 +++-- modules/nf-core/bcftools/index/main.nf | 5 +++-- modules/nf-core/bcftools/isec/main.nf | 5 +++-- modules/nf-core/bcftools/merge/main.nf | 5 +++-- modules/nf-core/bcftools/mpileup/main.nf | 5 +++-- modules/nf-core/bcftools/norm/main.nf | 5 +++-- modules/nf-core/bcftools/query/main.nf | 5 +++-- modules/nf-core/bcftools/reheader/main.nf | 5 +++-- modules/nf-core/bcftools/roh/main.nf | 5 +++-- modules/nf-core/bcftools/sort/main.nf | 5 +++-- modules/nf-core/bcftools/stats/main.nf | 5 +++-- modules/nf-core/bcftools/view/main.nf | 5 +++-- modules/nf-core/bedtools/bamtobed/main.nf | 5 +++-- modules/nf-core/bedtools/complement/main.nf | 5 +++-- modules/nf-core/bedtools/genomecov/main.nf | 5 +++-- modules/nf-core/bedtools/getfasta/main.nf | 5 +++-- modules/nf-core/bedtools/intersect/main.nf | 5 +++-- modules/nf-core/bedtools/makewindows/main.nf | 5 +++-- modules/nf-core/bedtools/maskfasta/main.nf | 5 +++-- modules/nf-core/bedtools/merge/main.nf | 5 +++-- modules/nf-core/bedtools/slop/main.nf | 5 +++-- modules/nf-core/bedtools/sort/main.nf | 5 +++-- modules/nf-core/bedtools/split/main.nf | 5 +++-- modules/nf-core/bedtools/subtract/main.nf | 5 +++-- modules/nf-core/biobambam/bammarkduplicates2/main.nf | 5 +++-- modules/nf-core/biobambam/bammerge/main.nf | 5 +++-- modules/nf-core/biobambam/bamsormadup/main.nf | 5 +++-- modules/nf-core/biscuit/align/main.nf | 5 +++-- modules/nf-core/biscuit/biscuitblaster/main.nf | 5 +++-- modules/nf-core/biscuit/bsconv/main.nf | 5 +++-- modules/nf-core/biscuit/epiread/main.nf | 5 +++-- modules/nf-core/biscuit/index/main.nf | 5 +++-- modules/nf-core/biscuit/mergecg/main.nf | 5 +++-- modules/nf-core/biscuit/pileup/main.nf | 5 +++-- modules/nf-core/biscuit/qc/main.nf | 5 +++-- modules/nf-core/biscuit/vcf2bed/main.nf | 5 +++-- modules/nf-core/bismark/align/main.nf | 5 +++-- modules/nf-core/bismark/deduplicate/main.nf | 5 +++-- modules/nf-core/bismark/genomepreparation/main.nf | 5 +++-- modules/nf-core/bismark/methylationextractor/main.nf | 5 +++-- modules/nf-core/bismark/report/main.nf | 5 +++-- modules/nf-core/bismark/summary/main.nf | 5 +++-- modules/nf-core/blast/blastn/main.nf | 5 +++-- modules/nf-core/blast/makeblastdb/main.nf | 5 +++-- modules/nf-core/blast/tblastn/main.nf | 5 +++-- modules/nf-core/bowtie/align/main.nf | 4 ++-- modules/nf-core/bowtie/build/main.nf | 4 ++-- modules/nf-core/bowtie2/align/main.nf | 5 +++-- modules/nf-core/bowtie2/build/main.nf | 5 +++-- modules/nf-core/bracken/bracken/main.nf | 5 +++-- modules/nf-core/bracken/combinebrackenoutputs/main.nf | 5 +++-- modules/nf-core/busco/main.nf | 5 +++-- modules/nf-core/bwa/aln/main.nf | 5 +++-- modules/nf-core/bwa/index/main.nf | 5 +++-- modules/nf-core/bwa/mem/main.nf | 5 +++-- modules/nf-core/bwa/sampe/main.nf | 5 +++-- modules/nf-core/bwa/samse/main.nf | 5 +++-- modules/nf-core/bwamem2/index/main.nf | 5 +++-- modules/nf-core/bwamem2/mem/main.nf | 5 +++-- modules/nf-core/bwameth/align/main.nf | 5 +++-- modules/nf-core/bwameth/index/main.nf | 5 +++-- modules/nf-core/cat/cat/main.nf | 5 +++-- modules/nf-core/cat/fastq/main.nf | 5 +++-- modules/nf-core/centrifuge/centrifuge/main.nf | 5 +++-- modules/nf-core/centrifuge/kreport/main.nf | 5 +++-- modules/nf-core/checkm/lineagewf/main.nf | 5 +++-- modules/nf-core/checkm/qa/main.nf | 5 +++-- modules/nf-core/chromap/chromap/main.nf | 5 +++-- modules/nf-core/chromap/index/main.nf | 5 +++-- modules/nf-core/clonalframeml/main.nf | 5 +++-- modules/nf-core/cmseq/polymut/main.nf | 5 +++-- modules/nf-core/cnvkit/antitarget/main.nf | 5 +++-- modules/nf-core/cnvkit/batch/main.nf | 5 +++-- modules/nf-core/cnvkit/reference/main.nf | 5 +++-- modules/nf-core/cnvpytor/callcnvs/main.nf | 5 +++-- modules/nf-core/cnvpytor/histogram/main.nf | 5 +++-- modules/nf-core/cnvpytor/importreaddepth/main.nf | 5 +++-- modules/nf-core/cnvpytor/partition/main.nf | 5 +++-- modules/nf-core/cnvpytor/view/main.nf | 5 +++-- modules/nf-core/controlfreec/assesssignificance/main.nf | 5 +++-- modules/nf-core/controlfreec/freec/main.nf | 5 +++-- modules/nf-core/controlfreec/freec2bed/main.nf | 5 +++-- modules/nf-core/controlfreec/freec2circos/main.nf | 5 +++-- modules/nf-core/controlfreec/makegraph/main.nf | 5 +++-- modules/nf-core/cooler/cload/main.nf | 5 +++-- modules/nf-core/cooler/digest/main.nf | 5 +++-- modules/nf-core/cooler/dump/main.nf | 5 +++-- modules/nf-core/cooler/merge/main.nf | 5 +++-- modules/nf-core/cooler/zoomify/main.nf | 5 +++-- modules/nf-core/crumble/main.nf | 5 +++-- modules/nf-core/csvtk/concat/main.nf | 5 +++-- modules/nf-core/csvtk/split/main.nf | 5 +++-- modules/nf-core/custom/dumpsoftwareversions/main.nf | 5 +++-- modules/nf-core/custom/getchromsizes/main.nf | 5 +++-- modules/nf-core/custom/sratoolsncbisettings/main.nf | 5 +++-- modules/nf-core/cutadapt/main.nf | 5 +++-- modules/nf-core/damageprofiler/main.nf | 5 +++-- modules/nf-core/dastool/dastool/main.nf | 5 +++-- modules/nf-core/dastool/fastatocontig2bin/main.nf | 5 +++-- modules/nf-core/dastool/scaffolds2bin/main.nf | 5 +++-- modules/nf-core/dedup/main.nf | 5 +++-- modules/nf-core/deeparg/downloaddata/main.nf | 5 +++-- modules/nf-core/deeparg/predict/main.nf | 5 +++-- modules/nf-core/deepbgc/download/main.nf | 5 +++-- modules/nf-core/deepbgc/pipeline/main.nf | 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| 5 +++-- modules/nf-core/gatk4/calculatecontamination/main.nf | 5 +++-- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 5 +++-- modules/nf-core/gatk4/collectreadcounts/main.nf | 5 +++-- modules/nf-core/gatk4/collectsvevidence/main.nf | 5 +++-- modules/nf-core/gatk4/combinegvcfs/main.nf | 5 +++-- modules/nf-core/gatk4/composestrtablefile/main.nf | 5 +++-- modules/nf-core/gatk4/createsequencedictionary/main.nf | 5 +++-- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 5 +++-- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 5 +++-- modules/nf-core/gatk4/fastqtosam/main.nf | 5 +++-- modules/nf-core/gatk4/filtermutectcalls/main.nf | 5 +++-- modules/nf-core/gatk4/filtervarianttranches/main.nf | 5 +++-- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 5 +++-- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 5 +++-- modules/nf-core/gatk4/genomicsdbimport/main.nf | 5 +++-- modules/nf-core/gatk4/genotypegvcfs/main.nf | 5 +++-- 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+++-- modules/nf-core/gatk4/splitncigarreads/main.nf | 5 +++-- modules/nf-core/gatk4/variantfiltration/main.nf | 5 +++-- modules/nf-core/gatk4/variantrecalibrator/main.nf | 5 +++-- modules/nf-core/gecco/run/main.nf | 5 +++-- modules/nf-core/genmap/index/main.nf | 5 +++-- modules/nf-core/genmap/mappability/main.nf | 5 +++-- modules/nf-core/genmod/annotate/main.nf | 5 +++-- modules/nf-core/genmod/compound/main.nf | 5 +++-- modules/nf-core/genmod/models/main.nf | 5 +++-- modules/nf-core/genmod/score/main.nf | 5 +++-- modules/nf-core/genomescope2/main.nf | 5 +++-- modules/nf-core/genotyphi/parse/main.nf | 5 +++-- modules/nf-core/genrich/main.nf | 5 +++-- modules/nf-core/gfaffix/main.nf | 5 +++-- modules/nf-core/gffread/main.nf | 5 +++-- modules/nf-core/glimpse/chunk/main.nf | 5 +++-- modules/nf-core/glnexus/main.nf | 5 +++-- modules/nf-core/goat/taxonsearch/main.nf | 5 +++-- modules/nf-core/graphmap2/align/main.nf | 5 +++-- modules/nf-core/graphmap2/index/main.nf | 5 +++-- 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modules/nf-core/picard/markduplicates/main.nf | 5 +++-- modules/nf-core/picard/mergesamfiles/main.nf | 5 +++-- modules/nf-core/picard/renamesampleinvcf/main.nf | 5 +++-- modules/nf-core/picard/sortsam/main.nf | 5 +++-- modules/nf-core/picard/sortvcf/main.nf | 5 +++-- modules/nf-core/pints/caller/main.nf | 5 +++-- modules/nf-core/pirate/main.nf | 5 +++-- modules/nf-core/plasmidfinder/main.nf | 5 +++-- modules/nf-core/plasmidid/main.nf | 5 +++-- modules/nf-core/plink/extract/main.nf | 5 +++-- modules/nf-core/plink/vcf/main.nf | 5 +++-- modules/nf-core/plink2/extract/main.nf | 5 +++-- modules/nf-core/plink2/score/main.nf | 5 +++-- modules/nf-core/plink2/vcf/main.nf | 5 +++-- modules/nf-core/pmdtools/filter/main.nf | 5 +++-- modules/nf-core/porechop/main.nf | 5 +++-- modules/nf-core/preseq/ccurve/main.nf | 5 +++-- modules/nf-core/preseq/lcextrap/main.nf | 5 +++-- modules/nf-core/prinseqplusplus/main.nf | 5 +++-- modules/nf-core/prodigal/main.nf | 5 +++-- modules/nf-core/prokka/main.nf | 5 +++-- modules/nf-core/pycoqc/main.nf | 5 +++-- modules/nf-core/pydamage/analyze/main.nf | 5 +++-- modules/nf-core/pydamage/filter/main.nf | 5 +++-- modules/nf-core/qcat/main.nf | 5 +++-- modules/nf-core/qualimap/bamqc/main.nf | 5 +++-- modules/nf-core/qualimap/bamqccram/main.nf | 5 +++-- modules/nf-core/qualimap/rnaseq/main.nf | 5 +++-- modules/nf-core/quast/main.nf | 5 +++-- modules/nf-core/racon/main.nf | 5 +++-- modules/nf-core/rapidnj/main.nf | 5 +++-- modules/nf-core/rasusa/main.nf | 5 +++-- modules/nf-core/raven/main.nf | 5 +++-- modules/nf-core/raxmlng/main.nf | 5 +++-- modules/nf-core/rgi/main/main.nf | 5 +++-- modules/nf-core/rhocall/annotate/main.nf | 5 +++-- modules/nf-core/rmarkdownnotebook/main.nf | 5 +++-- modules/nf-core/roary/main.nf | 5 +++-- modules/nf-core/rsem/calculateexpression/main.nf | 5 +++-- modules/nf-core/rsem/preparereference/main.nf | 5 +++-- modules/nf-core/rseqc/bamstat/main.nf | 5 +++-- modules/nf-core/rseqc/inferexperiment/main.nf | 5 +++-- modules/nf-core/rseqc/innerdistance/main.nf | 5 +++-- modules/nf-core/rseqc/junctionannotation/main.nf | 5 +++-- modules/nf-core/rseqc/junctionsaturation/main.nf | 5 +++-- modules/nf-core/rseqc/readdistribution/main.nf | 5 +++-- modules/nf-core/rseqc/readduplication/main.nf | 5 +++-- modules/nf-core/rseqc/tin/main.nf | 5 +++-- modules/nf-core/rtgtools/pedfilter/main.nf | 5 +++-- modules/nf-core/rtgtools/vcfeval/main.nf | 5 +++-- modules/nf-core/salmon/index/main.nf | 5 +++-- modules/nf-core/salmon/quant/main.nf | 5 +++-- modules/nf-core/samblaster/main.nf | 5 +++-- modules/nf-core/samtools/ampliconclip/main.nf | 5 +++-- modules/nf-core/samtools/bam2fq/main.nf | 5 +++-- modules/nf-core/samtools/collate/main.nf | 5 +++-- modules/nf-core/samtools/collatefastq/main.nf | 5 +++-- modules/nf-core/samtools/convert/main.nf | 5 +++-- modules/nf-core/samtools/depth/main.nf | 5 +++-- modules/nf-core/samtools/dict/main.nf | 5 +++-- modules/nf-core/samtools/faidx/main.nf | 5 +++-- modules/nf-core/samtools/fasta/main.nf | 5 +++-- modules/nf-core/samtools/fastq/main.nf | 5 +++-- modules/nf-core/samtools/fixmate/main.nf | 5 +++-- modules/nf-core/samtools/flagstat/main.nf | 5 +++-- modules/nf-core/samtools/getrg/main.nf | 5 +++-- modules/nf-core/samtools/idxstats/main.nf | 5 +++-- modules/nf-core/samtools/index/main.nf | 5 +++-- modules/nf-core/samtools/markdup/main.nf | 5 +++-- modules/nf-core/samtools/merge/main.nf | 5 +++-- modules/nf-core/samtools/mpileup/main.nf | 5 +++-- modules/nf-core/samtools/sort/main.nf | 5 +++-- modules/nf-core/samtools/stats/main.nf | 5 +++-- modules/nf-core/samtools/view/main.nf | 5 +++-- modules/nf-core/scoary/main.nf | 5 +++-- modules/nf-core/scramble/clusteranalysis/main.nf | 5 +++-- modules/nf-core/scramble/clusteridentifier/main.nf | 5 +++-- modules/nf-core/seacr/callpeak/main.nf | 5 +++-- modules/nf-core/seqkit/pair/main.nf | 5 +++-- modules/nf-core/seqkit/replace/main.nf | 5 +++-- modules/nf-core/seqkit/split2/main.nf | 5 +++-- modules/nf-core/seqkit/stats/main.nf | 5 +++-- modules/nf-core/seqsero2/main.nf | 5 +++-- modules/nf-core/seqtk/mergepe/main.nf | 5 +++-- modules/nf-core/seqtk/rename/main.nf | 5 +++-- modules/nf-core/seqtk/sample/main.nf | 5 +++-- modules/nf-core/seqtk/seq/main.nf | 5 +++-- modules/nf-core/seqtk/subseq/main.nf | 5 +++-- modules/nf-core/sequenzautils/bam2seqz/main.nf | 5 +++-- modules/nf-core/sequenzautils/gcwiggle/main.nf | 5 +++-- modules/nf-core/seqwish/induce/main.nf | 5 +++-- modules/nf-core/seroba/run/main.nf | 5 +++-- modules/nf-core/sexdeterrmine/main.nf | 5 +++-- modules/nf-core/shasta/main.nf | 5 +++-- modules/nf-core/shasum/main.nf | 5 +++-- modules/nf-core/shigatyper/main.nf | 5 +++-- modules/nf-core/shovill/main.nf | 5 +++-- modules/nf-core/sistr/main.nf | 5 +++-- modules/nf-core/slimfastq/main.nf | 5 +++-- modules/nf-core/snapaligner/align/main.nf | 5 +++-- modules/nf-core/snapaligner/index/main.nf | 5 +++-- modules/nf-core/snippy/core/main.nf | 5 +++-- modules/nf-core/snippy/run/main.nf | 5 +++-- modules/nf-core/snpdists/main.nf | 5 +++-- modules/nf-core/snpeff/main.nf | 5 +++-- modules/nf-core/snpsift/split/main.nf | 5 +++-- modules/nf-core/snpsites/main.nf | 5 +++-- modules/nf-core/somalier/extract/main.nf | 5 +++-- modules/nf-core/somalier/relate/main.nf | 5 +++-- modules/nf-core/sortmerna/main.nf | 5 +++-- modules/nf-core/sourmash/sketch/main.nf | 5 +++-- modules/nf-core/spades/main.nf | 5 +++-- modules/nf-core/spatyper/main.nf | 5 +++-- modules/nf-core/sratools/fasterqdump/main.nf | 5 +++-- modules/nf-core/sratools/prefetch/main.nf | 5 +++-- modules/nf-core/srst2/srst2/main.nf | 5 +++-- modules/nf-core/ssuissero/main.nf | 3 ++- modules/nf-core/stadeniolib/scramble/main.nf | 5 +++-- modules/nf-core/staphopiasccmec/main.nf | 5 +++-- modules/nf-core/star/align/main.nf | 5 +++-- modules/nf-core/star/genomegenerate/main.nf | 5 +++-- modules/nf-core/stranger/main.nf | 5 +++-- modules/nf-core/strelka/germline/main.nf | 5 +++-- modules/nf-core/strelka/somatic/main.nf | 5 +++-- modules/nf-core/stringtie/merge/main.nf | 5 +++-- modules/nf-core/stringtie/stringtie/main.nf | 5 +++-- modules/nf-core/subread/featurecounts/main.nf | 5 +++-- modules/nf-core/svdb/merge/main.nf | 5 +++-- modules/nf-core/svdb/query/main.nf | 5 +++-- modules/nf-core/svtk/standardize/main.nf | 5 +++-- modules/nf-core/tabix/bgzip/main.nf | 5 +++-- modules/nf-core/tabix/bgziptabix/main.nf | 5 +++-- modules/nf-core/tabix/tabix/main.nf | 5 +++-- modules/nf-core/tailfindr/main.nf | 5 +++-- modules/nf-core/tbprofiler/profile/main.nf | 5 +++-- modules/nf-core/tiddit/cov/main.nf | 5 +++-- modules/nf-core/tiddit/sv/main.nf | 5 +++-- modules/nf-core/transdecoder/longorf/main.nf | 5 +++-- modules/nf-core/transdecoder/predict/main.nf | 5 +++-- modules/nf-core/trimgalore/main.nf | 5 +++-- modules/nf-core/trimmomatic/main.nf | 5 +++-- modules/nf-core/ucsc/bedclip/main.nf | 5 +++-- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 5 +++-- modules/nf-core/ucsc/bedtobigbed/main.nf | 5 +++-- modules/nf-core/ucsc/bigwigaverageoverbed/main.nf | 5 +++-- modules/nf-core/ucsc/liftover/main.nf | 5 +++-- modules/nf-core/ucsc/wigtobigwig/main.nf | 5 +++-- modules/nf-core/ultra/align/main.nf | 5 +++-- modules/nf-core/ultra/index/main.nf | 5 +++-- modules/nf-core/ultra/pipeline/main.nf | 5 +++-- modules/nf-core/umitools/dedup/main.nf | 5 +++-- modules/nf-core/umitools/extract/main.nf | 5 +++-- modules/nf-core/unicycler/main.nf | 5 +++-- modules/nf-core/untar/main.nf | 5 +++-- modules/nf-core/unzip/main.nf | 5 +++-- modules/nf-core/vardictjava/main.nf | 5 +++-- modules/nf-core/variantbam/main.nf | 5 +++-- modules/nf-core/vcf2db/main.nf | 5 +++-- modules/nf-core/vcf2maf/main.nf | 5 +++-- modules/nf-core/vcfanno/main.nf | 5 +++-- modules/nf-core/vcflib/vcfbreakmulti/main.nf | 5 +++-- modules/nf-core/vcflib/vcfuniq/main.nf | 5 +++-- modules/nf-core/vcftools/main.nf | 5 +++-- modules/nf-core/verifybamid/verifybamid2/main.nf | 5 +++-- modules/nf-core/vsearch/sintax/main.nf | 5 +++-- modules/nf-core/vsearch/usearchglobal/main.nf | 5 +++-- modules/nf-core/wgsim/main.nf | 5 +++-- modules/nf-core/whamg/main.nf | 5 +++-- modules/nf-core/yara/index/main.nf | 5 +++-- modules/nf-core/yara/mapper/main.nf | 5 +++-- 616 files changed, 1845 insertions(+), 1231 deletions(-) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index 5e0f28f98e1..ab957c095f4 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -3,8 +3,9 @@ process ABACAS { label 'process_medium' conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) - def container_image = "/abacas:1.3.1--pl526_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "abacas:1.3.1--pl526_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index a86716affce..a3780f3fbf5 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -3,8 +3,9 @@ process ABRICATE_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - def container_image = "/abricate:1.0.1--ha8f3691_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "abricate:1.0.1--ha8f3691_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index 76fa5fd51dc..ab1f7dfa965 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -3,8 +3,9 @@ process ABRICATE_SUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) - def container_image = "/abricate:1.0.1--ha8f3691_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "abricate:1.0.1--ha8f3691_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 692beeb33af..e792330df0d 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -3,8 +3,9 @@ process ADAPTERREMOVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null) - def container_image = "/adapterremoval:2.3.2--hb7ba0dd_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "adapterremoval:2.3.2--hb7ba0dd_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 373622dc139..9cf5ebb3167 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -4,8 +4,9 @@ process ADAPTERREMOVALFIXPREFIX { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null) - def container_image = "/adapterremovalfixprefix:0.0.5--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "adapterremovalfixprefix:0.0.5--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 39f5b1c3615..3ff000f21de 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -3,8 +3,9 @@ process AGRVATE { label 'process_low' conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null) - def container_image = "/agrvate:1.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "agrvate:1.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index 4f85ae6ad68..6e4803ece3e 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -3,8 +3,9 @@ process ALLELECOUNTER { label 'process_low' conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null) - def container_image = "/cancerit-allelecount:4.3.0--h41abebc_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cancerit-allelecount:4.3.0--h41abebc_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index b9641759dd5..ac80298f05a 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -3,8 +3,9 @@ process AMPIR { label 'process_single' conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) - def container_image = "/r-ampir:1.1.0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "r-ampir:1.1.0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 8a11242273d..940a78c1ef2 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -4,8 +4,9 @@ process AMPLIFY_PREDICT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null) - def container_image = "/amplify:1.0.3--py36hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "amplify:1.0.3--py36hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(faa) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index ee27f3f3dd1..8f437f1f45f 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -2,8 +2,9 @@ process AMPS { label 'process_low' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - def container_image = "/hops:0.35--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hops:0.35--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path maltextract_results diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 8180999ee80..ae4f77df085 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -3,8 +3,9 @@ process AMRFINDERPLUS_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ncbi-amrfinderplus:3.10.30--h6e70893_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 72c6b316c1c..5f2ea0c8d58 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -3,8 +3,9 @@ process AMRFINDERPLUS_UPDATE { label 'process_single' conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null) - def container_image = "/ncbi-amrfinderplus:3.10.30--h6e70893_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ncbi-amrfinderplus:3.10.30--h6e70893_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + output: path "amrfinderdb.tar.gz", emit: db diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index bfe1bdef1cc..bd6f6dffb34 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -3,8 +3,9 @@ process ANGSD_DOCOUNTS { label 'process_low' conda (params.enable_conda ? "bioconda::angsd=0.939" : null) - def container_image = "/angsd:0.939--h468462d_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "angsd:0.939--h468462d_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 1f386692b83..8132ee9ca16 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -3,8 +3,9 @@ process ANTISMASH_ANTISMASHLITE { label 'process_medium' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "antismash-lite:6.0.1--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + containerOptions { workflow.containerEngine == 'singularity' ? diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 5185eb42175..00249d481b4 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,8 +2,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { label 'process_single' conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null) - def container_image = "/antismash-lite:6.0.1--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "antismash-lite:6.0.1--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 55f10f6cf8f..0bd96d4baf7 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -4,8 +4,9 @@ process ARIA2 { label 'process_single' conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null) - def container_image = "/aria2:1.36.0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "aria2:1.36.0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index 38b50930cc3..b4adfec2e32 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -3,8 +3,9 @@ process ARIBA_GETREF { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - def container_image = "/ariba:2.14.6--py39h67e14b5_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ariba:2.14.6--py39h67e14b5_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 0fd602ff8fb..3686e776896 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -3,8 +3,9 @@ process ARIBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null) - def container_image = "/ariba:2.14.6--py39h67e14b5_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ariba:2.14.6--py39h67e14b5_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 49d0f6ebb1a..1edcab1e1b9 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -3,8 +3,9 @@ process ARRIBA { label 'process_medium' conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null) - def container_image = "/arriba:2.3.0--haa8aa89_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "arriba:2.3.0--haa8aa89_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index b7103f212bb..2f18199e6aa 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -3,8 +3,9 @@ process ARTIC_GUPPYPLEX { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - def container_image = "/artic:1.2.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "artic:1.2.2--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index fd9d38f54d1..5a6f3e09ad6 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -3,8 +3,9 @@ process ARTIC_MINION { label 'process_high' conda (params.enable_conda ? "bioconda::artic=1.2.2" : null) - def container_image = "/artic:1.2.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "artic:1.2.2--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index 3dcb3240176..eae9f5ee0fb 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -3,8 +3,9 @@ process ASCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null) - def container_image = "/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 2e04c149f45..4d909e66785 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -3,8 +3,9 @@ process ASSEMBLYSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null) - def container_image = "/assembly-scan:0.4.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "assembly-scan:0.4.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index df5dd589db2..b39bb5c8b8f 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -3,8 +3,9 @@ process ATAQV_ATAQV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - def container_image = "/ataqv:1.3.0--py39hccc85d7_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ataqv:1.3.0--py39hccc85d7_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(peak_file) diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index a45a63f76db..5a98b849ff0 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -2,8 +2,9 @@ process ATAQV_MKARV { label 'process_medium' conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null) - def container_image = "/ataqv:1.3.0--py39hccc85d7_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ataqv:1.3.0--py39hccc85d7_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index b278fe0c8fa..64250b28f01 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -3,8 +3,9 @@ process ATLAS_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "atlas:0.9.9--h082e891_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index 1d2f542800e..be60c87e9d5 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -3,8 +3,9 @@ process ATLAS_PMD { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "atlas:0.9.9--h082e891_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index e487b5a5e99..ded7aaa498d 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -3,8 +3,9 @@ process ATLAS_RECAL { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "atlas:0.9.9--h082e891_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index e6a93a1c436..a3fcb66c732 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -3,8 +3,9 @@ process ATLAS_SPLITMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null) - def container_image = "/atlas:0.9.9--h082e891_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "atlas:0.9.9--h082e891_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index a2f36f22304..6dab17a956b 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -3,8 +3,9 @@ process BAKTA { label 'process_medium' conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) - def container_image = "/bakta:1.5.0--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bakta:1.5.0--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index f5039580cd9..34e42443eda 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -3,8 +3,9 @@ process BAMALIGNCLEANER { label 'process_low' conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null) - def container_image = "/bamaligncleaner:0.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bamaligncleaner:0.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index e6bae7ffaea..58e5f96d1a8 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -3,8 +3,9 @@ process BAMCMP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null) - def container_image = "/bamcmp:2.2--h05f6578_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bamcmp:2.2--h05f6578_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index 7fb6588e0d1..efa414adec4 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -3,8 +3,9 @@ process BAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - def container_image = "/bamtools:2.5.1--h9a82719_9" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bamtools:2.5.1--h9a82719_9" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index cd4120d5b52..559f72c33c7 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -3,8 +3,9 @@ process BAMTOOLS_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) - def container_image = "/bamtools:2.5.2--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bamtools:2.5.2--hd03093a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index a686f37c8f7..75a0c6820ca 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -3,8 +3,9 @@ process BAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) - def container_image = "/bamtools:2.5.1--h9a82719_9" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bamtools:2.5.1--h9a82719_9" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 767b821510d..89fe23b294e 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -3,8 +3,9 @@ process BAMUTIL_TRIMBAM { label 'process_single' conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null) - def container_image = "/bamutil:1.0.15--h2e03b76_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bamutil:1.0.15--h2e03b76_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 173f8dd8298..5c04969a6cd 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -3,8 +3,9 @@ process BANDAGE_IMAGE { label 'process_low' conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) - def container_image = "/bandage:0.8.1--hc9558a2_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bandage:0.8.1--hc9558a2_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 8bf12c5975f..05f109596a3 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -3,8 +3,9 @@ process BBMAP_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index a9be0864f8b..6080471700c 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -3,8 +3,9 @@ process BBMAP_BBDUK { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) - def container_image = "/bbmap:38.90--he522d1c_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bbmap:38.90--he522d1c_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 287de1fffce..6afe361d2c4 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,8 +2,9 @@ process BBMAP_BBSPLIT { label 'process_high' conda (params.enable_conda ? "bioconda::bbmap=38.93" : null) - def container_image = "/bbmap:38.93--he522d1c_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bbmap:38.93--he522d1c_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index 8183ff129d4..ef7b4deba43 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -4,8 +4,9 @@ process BBMAP_CLUMPIFY { label 'process_high_memory' conda (params.enable_conda ? "bioconda::bbmap=38.98" : null) - def container_image = "/bbmap:38.98--h5c4e2a8_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bbmap:38.98--h5c4e2a8_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index 9887f0add27..e2e5ccd6c66 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -3,8 +3,9 @@ process BBMAP_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::bbmap=38.92" : null) - def container_image = "/bbmap:38.92--he522d1c_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bbmap:38.92--he522d1c_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 15504d3f7d7..4ff7f61f5fc 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -3,8 +3,9 @@ process BBMAP_PILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null) - def container_image = "/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 8ef222462a0..8a7bb4985d7 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_ANNOTATE { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 934ba4640e2..247424bf243 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_CONCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index f8939b6775f..e70a473a197 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index 2d9034a3824..831805d1c88 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_CONVERT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 7deb4c91a03..3940b137c3a 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 3c49d6c5e68..968617d6a0a 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 27832fd30f8..76969f3393a 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_ISEC { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 91931601a07..326746ff691 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_MERGE { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index b41b3e349ff..da7e9c6ab52 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_MPILEUP { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index a1754c6097d..7cf5f8c76b5 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_NORM { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 826eed5cdff..0935ef2ca7f 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 3a996aa0b27..fbf02b8e378 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_REHEADER { label 'process_low' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index d09ede97182..27a57b42700 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_ROH { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 926a4e1f314..f446531eab4 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index e9569da3cbe..ef6430dbdca 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 3e7b8e2786c..1ada6d985a1 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -3,8 +3,9 @@ process BCFTOOLS_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null) - def container_image = "/bcftools:1.15.1--h0ea216a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bcftools:1.15.1--h0ea216a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(index) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index 63b0b7a29e5..b7ef343cf75 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_BAMTOBED { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index 70cfced86f3..4b8011eb095 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_COMPLEMENT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index a1c15efed49..f49bcf61d88 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 263b1d9de27..cd054ea20a4 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_GETFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path bed diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index a6fc8f7d54e..56a36f78e4d 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_INTERSECT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index 30b76025828..8afd2b5bef8 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_MAKEWINDOWS { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--h7d7f7ad_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--h7d7f7ad_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(regions) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index 7f4b4a7556e..a2fb3867ca9 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_MASKFASTA { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 2ab5f472b07..272f6706d3b 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index d538e87bb82..38225e46e47 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_SLOP { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 2376227ca93..091cc2892c0 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_SORT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index 9d116139d34..9a88212efa3 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_SPLIT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--h468198e_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--h468198e_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index 0cb02fd110f..94a35d2dc83 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -3,8 +3,9 @@ process BEDTOOLS_SUBTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) - def container_image = "/bedtools:2.30.0--hc088bd4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bedtools:2.30.0--hc088bd4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/modules/nf-core/biobambam/bammarkduplicates2/main.nf index a72be6a2242..6e841a2e148 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -3,8 +3,9 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 { label 'process_medium' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - def container_image = "/biobambam:2.0.183--h9f5acd7_1" - container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) + def container_image = "biobambam:2.0.183--h9f5acd7_1" + container (params.container_registry ?: 'quay.io/biocontainers' , container_image) + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index 13e7b17efbb..ed4303bf071 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -3,8 +3,9 @@ process BIOBAMBAM_BAMMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - def container_image = "/biobambam:2.0.183--h9f5acd7_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "biobambam:2.0.183--h9f5acd7_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index 1073da0ba3e..9982e67f600 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -3,8 +3,9 @@ process BIOBAMBAM_BAMSORMADUP { label "process_medium" conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null) - def container_image = "/biobambam:2.0.183--h9f5acd7_1" - container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) + def container_image = "biobambam:2.0.183--h9f5acd7_1" + container (params.container_registry ?: 'quay.io/biocontainers' , container_image) + input: tuple val(meta), path(bams, stageAs: "?/*") diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index 95aa4fa06cf..36d8325c992 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -3,8 +3,9 @@ process BISCUIT_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index bc9b6992ff1..47ea80305bb 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -3,8 +3,9 @@ process BISCUIT_BLASTER { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index 290fae18774..08a7b6e1bf4 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -3,8 +3,9 @@ process BISCUIT_BSCONV { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "biscuit:1.0.2.20220113--h81a5ba2_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index 06780e35cfa..748a08cae6d 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -3,8 +3,9 @@ process BISCUIT_EPIREAD { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(snp_bed) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index b5cf5917efa..63d50a23802 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -3,8 +3,9 @@ process BISCUIT_INDEX { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "biscuit:1.0.2.20220113--h81a5ba2_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index eb7e2175654..d73d86b1fa9 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -3,8 +3,9 @@ process BISCUIT_MERGECG { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 15839eb00ab..2d5ac26234a 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -3,8 +3,9 @@ process BISCUIT_PILEUP { label 'process_high' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index efbe6afaa57..882c0a802f4 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -3,8 +3,9 @@ process BISCUIT_QC { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null) - def container_image = "/biscuit:1.0.2.20220113--h81a5ba2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "biscuit:1.0.2.20220113--h81a5ba2_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index af7fc7d6db0..c4148ae93f1 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -3,8 +3,9 @@ process BISCUIT_VCF2BED { label 'process_long' conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null) - def container_image = "/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index 6922160ed5d..b6698b9e1fe 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -3,8 +3,9 @@ process BISMARK_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bismark:0.23.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index b3dc6d9a502..e86dc33363e 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -3,8 +3,9 @@ process BISMARK_DEDUPLICATE { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bismark:0.23.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 85619f385f3..de6694ce7ee 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -3,8 +3,9 @@ process BISMARK_GENOMEPREPARATION { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bismark:0.23.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 1012bd2ed27..9ba0a90d262 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -3,8 +3,9 @@ process BISMARK_METHYLATIONEXTRACTOR { label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bismark:0.23.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 80307f9531d..743ef6519c2 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -3,8 +3,9 @@ process BISMARK_REPORT { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bismark:0.23.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index a760dc4f3f8..217f0aea9c1 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -2,8 +2,9 @@ process BISMARK_SUMMARY { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) - def container_image = "/bismark:0.23.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bismark:0.23.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path(bam) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index b4f5e5eb22f..ace1c541a5b 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -3,8 +3,9 @@ process BLAST_BLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - def container_image = "/blast:2.12.0--pl5262h3289130_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "blast:2.12.0--pl5262h3289130_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 0f7f3a86b9f..1920d31d168 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -3,8 +3,9 @@ process BLAST_MAKEBLASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - def container_image = "/blast:2.12.0--pl5262h3289130_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "blast:2.12.0--pl5262h3289130_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index 9e4afb475ff..a5b9e9ef3b6 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -3,8 +3,9 @@ process BLAST_TBLASTN { label 'process_medium' conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null) - def container_image = "/blast:2.12.0--pl5262h3289130_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "blast:2.12.0--pl5262h3289130_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index af0ccc20463..00521da381d 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -3,8 +3,8 @@ process BOWTIE_ALIGN { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null) - def container_image = "/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" - container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) + def container_image = "mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 4ae0d635adc..252608dafff 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -3,8 +3,8 @@ process BOWTIE_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) - def container_image = "/bowtie:1.3.0--py38hed8969a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bowtie:1.3.0--py38hed8969a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') input: path fasta diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index be80dbdba95..83af7b58777 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -3,8 +3,9 @@ process BOWTIE2_ALIGN { label "process_high" conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null) - def container_image = "/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" - container ((params.container_registry ?: 'quay.io/biocontainers') + container_image) + def container_image = "mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 8d28546d4c2..95e1819e624 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -3,8 +3,9 @@ process BOWTIE2_BUILD { label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) - def container_image = "/bowtie2:2.4.4--py39hbb4e92a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bowtie2:2.4.4--py39hbb4e92a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index aaa70a7c538..894ce014b2a 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -5,8 +5,9 @@ process BRACKEN_BRACKEN { // WARN: Version information not provided by tool on CLI. // Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - def container_image = "/bracken:2.7--py39hc16433a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bracken:2.7--py39hc16433a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(kraken_report) diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index f289c11a309..825c1b02ad8 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,8 +2,9 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { label 'process_low' conda (params.enable_conda ? "bioconda::bracken=2.7" : null) - def container_image = "/bracken:2.7--py39hc16433a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bracken:2.7--py39hc16433a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index dad9c36d1bd..3d6af2f93bc 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -3,8 +3,9 @@ process BUSCO { label 'process_medium' conda (params.enable_conda ? "bioconda::busco=5.4.3" : null) - def container_image = "/busco:5.4.3--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "busco:5.4.3--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path('tmp_input/*') diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 446606ebf18..68df053560e 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -3,8 +3,9 @@ process BWA_ALN { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - def container_image = "/bwa:0.7.17--h5bf99c6_8" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bwa:0.7.17--h5bf99c6_8" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index b588cd4859b..059264dde20 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -3,8 +3,9 @@ process BWA_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - def container_image = "/bwa:0.7.17--hed695b0_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bwa:0.7.17--hed695b0_7" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 9cf25e101da..8dd91f17ff7 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -3,8 +3,9 @@ process BWA_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index f882d945c86..ba7079bc943 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -3,8 +3,9 @@ process BWA_SAMPE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 3a3f6f455d4..9288d3e5ad7 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -3,8 +3,9 @@ process BWA_SAMSE { label 'process_medium' conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 9b142ff3cd4..3c6f581535e 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -3,8 +3,9 @@ process BWAMEM2_INDEX { label 'process_single' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) - def container_image = "/bwa-mem2:2.2.1--he513fc3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bwa-mem2:2.2.1--he513fc3_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 6f9e93d98eb..2937601dd8a 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -3,8 +3,9 @@ process BWAMEM2_MEM { label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index df4a7a948ff..e81fcf8060c 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -3,8 +3,9 @@ process BWAMETH_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - def container_image = "/bwameth:0.2.2--py_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bwameth:0.2.2--py_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index bfff95518cc..733e622783d 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -3,8 +3,9 @@ process BWAMETH_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) - def container_image = "/bwameth:0.2.2--py_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "bwameth:0.2.2--py_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index a302cfb21d4..ef103fa8417 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -3,8 +3,9 @@ process CAT_CAT { label 'process_low' conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null) - def container_image = "/pigz:2.3.4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pigz:2.3.4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 016c8a61fb7..44aea437a90 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,8 +3,9 @@ process CAT_FASTQ { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: '' + container_image) } + def container_image = "ubuntu:20.04" + container [ params.container_registry ?: '' , container_image ].join('/') + input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index c3bda72b511..d3b45c597df 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -3,8 +3,9 @@ process CENTRIFUGE_CENTRIFUGE { label 'process_high' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "centrifuge:1.0.4_beta--h9a82719_6" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index eef2696eb72..b947befa973 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -3,8 +3,9 @@ process CENTRIFUGE_KREPORT { label 'process_single' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) - def container_image = "/centrifuge:1.0.4_beta--h9a82719_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "centrifuge:1.0.4_beta--h9a82719_6" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index 675c04203f2..f9e8fe7e977 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -3,8 +3,9 @@ process CHECKM_LINEAGEWF { label 'process_medium' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "checkm-genome:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 7bf71a35a3c..69ba63b73f0 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -3,8 +3,9 @@ process CHECKM_QA { label 'process_low' conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null) - def container_image = "/checkm-genome:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "checkm-genome:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index 721b3c5333b..a88f8d50d14 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -3,8 +3,9 @@ process CHROMAP_CHROMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index a56afc3ec8f..375b196ed1c 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -3,8 +3,9 @@ process CHROMAP_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) - def container_image = "/chromap:0.2.1--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "chromap:0.2.1--hd03093a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 38508c003dd..11f9668f8fa 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -3,8 +3,9 @@ process CLONALFRAMEML { label 'process_low' conda (params.enable_conda ? "bioconda::clonalframeml=1.12" : null) - def container_image = "/clonalframeml:1.12--h7d875b9_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "clonalframeml:1.12--h7d875b9_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index c07276534f2..e48cd7eb459 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -4,8 +4,9 @@ process CMSEQ_POLYMUT { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null) - def container_image = "/cmseq:1.0.4--pyhb7b1952_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cmseq:1.0.4--pyhb7b1952_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index 521143e0f37..b0d8e1f667e 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -3,8 +3,9 @@ process CNVKIT_ANTITARGET { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvkit:0.9.9--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index fa6a30ed9b2..251e81df21b 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -3,8 +3,9 @@ process CNVKIT_BATCH { label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) - def container_image = "/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index bc727cebc01..3dbc3b832fb 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -3,8 +3,9 @@ process CNVKIT_REFERENCE { label 'process_low' conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null) - def container_image = "/cnvkit:0.9.9--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvkit:0.9.9--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index 74e5e8332b4..d2303b8b5a0 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -3,8 +3,9 @@ process CNVPYTOR_CALLCNVS { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index 609fbe8a9a0..c73dc3f006b 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -3,8 +3,9 @@ process CNVPYTOR_HISTOGRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index 3899e065cb8..ad3ec0420bd 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -3,8 +3,9 @@ process CNVPYTOR_IMPORTREADDEPTH { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_file), path(index) diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index fbb699192b9..b89c8e07804 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -3,8 +3,9 @@ process CNVPYTOR_PARTITION { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pytor) diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index 77fd85cfa8d..abe3a354c8b 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -3,8 +3,9 @@ process CNVPYTOR_VIEW { label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null) - def container_image = "/cnvpytor:1.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pytor_files) diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index c7f21fdf527..3c15400d4df 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -3,8 +3,9 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "control-freec:11.6--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 342983de63c..130106ef791 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -3,8 +3,9 @@ process CONTROLFREEC_FREEC { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "control-freec:11.6--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index ab6218f9d37..c9ed01a7991 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -3,8 +3,9 @@ process CONTROLFREEC_FREEC2BED { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "control-freec:11.6--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 951115daa51..367b4094534 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -3,8 +3,9 @@ process CONTROLFREEC_FREEC2CIRCOS { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "control-freec:11.6--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index be4d359a1af..743e650dcc5 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -3,8 +3,9 @@ process CONTROLFREEC_MAKEGRAPH { label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) - def container_image = "/control-freec:11.6--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "control-freec:11.6--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 51d7b7a0727..751ed796acd 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -3,8 +3,9 @@ process COOLER_CLOAD { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cooler:0.8.11--pyh3252c3a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pairs), path(index) diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index 7c4e30ce820..15ebb7659e5 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -3,8 +3,9 @@ process COOLER_DIGEST { label 'process_medium' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cooler:0.8.11--pyh3252c3a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index 0bdeef9bdf6..33a075a197c 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -3,8 +3,9 @@ process COOLER_DUMP { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cooler:0.8.11--pyh3252c3a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index 1018657a78a..0ae64fdb9cd 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -3,8 +3,9 @@ process COOLER_MERGE { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cooler:0.8.11--pyh3252c3a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index c5a19fed4cb..39a128f5665 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -3,8 +3,9 @@ process COOLER_ZOOMIFY { label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) - def container_image = "/cooler:0.8.11--pyh3252c3a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cooler:0.8.11--pyh3252c3a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index b0481e9b1a8..d8a3a4fcaee 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -3,8 +3,9 @@ process CRUMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::crumble=0.9.0" : null) - def container_image = "/crumble:0.9.0--hb0d9459_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "crumble:0.9.0--hb0d9459_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 02c49d2d820..1ba8f7b6004 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -3,8 +3,9 @@ process CSVTK_CONCAT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - def container_image = "/csvtk:0.23.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "csvtk:0.23.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(csv) diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 15e3f27b9a7..70766855f35 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -3,8 +3,9 @@ process CSVTK_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) - def container_image = "/csvtk:0.23.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "csvtk:0.23.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(csv) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 7ea35504ce8..ebe91c8d39b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -3,8 +3,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - def container_image = "/multiqc:1.13--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "multiqc:1.13--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 72950bc8f66..6007e5e278c 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -3,8 +3,9 @@ process CUSTOM_GETCHROMSIZES { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 508f303e24c..4b7a3faebce 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -3,8 +3,9 @@ process CUSTOM_SRATOOLSNCBISETTINGS { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sra-tools:2.11.0--pl5321ha49a11a_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + output: path('*.mkfg') , emit: ncbi_settings diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 8643ceb5f73..0001f6dfd12 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -3,8 +3,9 @@ process CUTADAPT { label 'process_medium' conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) - def container_image = "/cutadapt:3.4--py39h38f01e4_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "cutadapt:3.4--py39h38f01e4_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index 4ccc68c0d60..d3dd3afda34 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -3,8 +3,9 @@ process DAMAGEPROFILER { label 'process_single' conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) - def container_image = "/damageprofiler:1.1--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "damageprofiler:1.1--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index 48a3f5b8d57..bc3d6442147 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -3,8 +3,9 @@ process DASTOOL_DASTOOL { label 'process_medium' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - def container_image = "/das_tool:1.1.4--r41hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "das_tool:1.1.4--r41hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(contigs), path(bins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index 0f2c819c71d..247129c205a 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -3,8 +3,9 @@ process DASTOOL_FASTATOCONTIG2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null) - def container_image = "/das_tool:1.1.4--r41hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "das_tool:1.1.4--r41hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index d1697b9f1d6..5f432d8b1f3 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -3,8 +3,9 @@ process DASTOOL_SCAFFOLDS2BIN { label 'process_single' conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) - def container_image = "/das_tool:1.1.3--r41hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "das_tool:1.1.3--r41hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index cd3f006fef6..2516897ce65 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -3,8 +3,9 @@ process DEDUP { label 'process_single' conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null) - def container_image = "/dedup:0.12.8--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dedup:0.12.8--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index ee8953b2597..74a1c347910 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,8 +2,9 @@ process DEEPARG_DOWNLOADDATA { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - def container_image = "/deeparg:1.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deeparg:1.0.2--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 135d75014c5..32e76c4a2ef 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -3,8 +3,9 @@ process DEEPARG_PREDICT { label 'process_single' conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null) - def container_image = "/deeparg:1.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deeparg:1.0.2--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + /* We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index 7a07b7c6f01..d7fde0fa9f2 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -2,8 +2,9 @@ process DEEPBGC_DOWNLOAD { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deepbgc:0.1.30--pyhb7b1952_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + output: path "deepbgc_db/" , emit: db diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index f07619125ef..d56d4e66a6b 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -3,8 +3,9 @@ process DEEPBGC_PIPELINE { label 'process_single' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) - def container_image = "/deepbgc:0.1.30--pyhb7b1952_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deepbgc:0.1.30--pyhb7b1952_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(genome) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 8f8a2a703ec..2581fa4c5f9 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_BAMCOVERAGE { label 'process_low' conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index 90175ee126e..b7b5fa2d80c 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_COMPUTEMATRIX { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deeptools:3.5.1--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bigwig) diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index 98b65ee43ac..fc866886d30 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_PLOTFINGERPRINT { label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deeptools:3.5.1--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index c612b271ef3..e9066f99c46 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_PLOTHEATMAP { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deeptools:3.5.1--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index c3454dc913f..138bebc4cf4 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -3,8 +3,9 @@ process DEEPTOOLS_PLOTPROFILE { label 'process_low' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) - def container_image = "/deeptools:3.5.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "deeptools:3.5.1--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index 972165afc43..fc1fe06638f 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -3,8 +3,9 @@ process DELLY_CALL { label 'process_medium' conda (params.enable_conda ? "bioconda::delly=1.1.5" : null) - def container_image = "/delly:1.1.5--h358d541_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "delly:1.1.5--h358d541_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(exclude_bed) diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index b8cdadcf157..b80cf19035b 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -3,8 +3,9 @@ process DIAMOND_BLASTP { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - def container_image = "/diamond:2.0.15--hb97b32f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "diamond:2.0.15--hb97b32f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 3fe5ef002f0..6598e4d01a3 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -3,8 +3,9 @@ process DIAMOND_BLASTX { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - def container_image = "/diamond:2.0.15--hb97b32f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "diamond:2.0.15--hb97b32f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index 33764cc226a..91d5c88ecb0 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -3,8 +3,9 @@ process DIAMOND_MAKEDB { label 'process_medium' conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) - def container_image = "/diamond:2.0.15--hb97b32f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "diamond:2.0.15--hb97b32f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index 7d66c0fe322..ea70899eda0 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -3,8 +3,9 @@ process DRAGMAP_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null) - def container_image = "/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 7f2b88bc476..3cb527fd11d 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -3,8 +3,9 @@ process DRAGMAP_HASHTABLE { label 'process_high' conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null) - def container_image = "/dragmap:1.2.1--hd4ca14e_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dragmap:1.2.1--hd4ca14e_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index af6c96cc7bc..90ed9f6baf7 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -3,8 +3,9 @@ process DRAGONFLYE { label 'process_medium' conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null) - def container_image = "/dragonflye:1.0.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dragonflye:1.0.11--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 982cdbcc254..19a3c6ca333 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -3,8 +3,9 @@ process DSHBIO_EXPORTSEGMENTS { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dsh-bio:2.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index f7e4ca41cf6..2f3c6fe5298 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -3,8 +3,9 @@ process DSHBIO_FILTERBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dsh-bio:2.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index c12b652153d..2e317fb6c5e 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -3,8 +3,9 @@ process DSHBIO_FILTERGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dsh-bio:2.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index 8f737061a93..2452eb1736b 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -3,8 +3,9 @@ process DSHBIO_SPLITBED { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dsh-bio:2.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 9e87d5fddf2..1cb7c12e78f 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -3,8 +3,9 @@ process DSHBIO_SPLITGFF3 { label 'process_medium' conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null) - def container_image = "/dsh-bio:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "dsh-bio:2.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index f3cee14d68f..123ea9323ab 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -3,8 +3,9 @@ process ECTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ectyper=1.0.0" : null) - def container_image = "/ectyper:1.0.0--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ectyper:1.0.0--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 91ab2e0bc92..2ef4d91700f 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -3,8 +3,9 @@ process ELPREP_FILTER { label 'process_high' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - def container_image = "/elprep:5.1.2--he881be0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "elprep:5.1.2--he881be0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index 286610269d7..225ff61efab 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -3,8 +3,9 @@ process ELPREP_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - def container_image = "/elprep:5.1.2--he881be0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "elprep:5.1.2--he881be0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index 0578226659b..a48a961c30e 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -3,8 +3,9 @@ process ELPREP_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) - def container_image = "/elprep:5.1.2--he881be0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "elprep:5.1.2--he881be0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 1d3ff7e8770..9c6ff155189 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -3,8 +3,9 @@ process EMBOSS_SEQRET { label 'process_single' conda (params.enable_conda ? "bioconda::emboss=6.6.0" : null) - def container_image = "/emboss:6.6.0--hf657eab_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "emboss:6.6.0--hf657eab_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 37d9c30b2e8..018c0fca675 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -3,8 +3,9 @@ process EMMTYPER { label 'process_low' conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null) - def container_image = "/emmtyper:0.2.0--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "emmtyper:0.2.0--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index ad60dc6e453..9730ee7a554 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -3,8 +3,9 @@ process ENDORSPY { label 'process_low' conda (params.enable_conda ? "bioconda::endorspy=0.4" : null) - def container_image = "/endorspy:0.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "endorspy:0.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index e5154508187..8e58e386151 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -3,8 +3,9 @@ process ENSEMBLVEP { label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) - def container_image = "/ensembl-vep:106.1--pl5321h4a94de4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ensembl-vep:106.1--pl5321h4a94de4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index 855ba93627e..ece9777bd0f 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -3,8 +3,9 @@ process ENTREZDIRECT_ESEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - def container_image = "/entrez-direct:16.2--he881be0_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "entrez-direct:16.2--he881be0_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), val(term) diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index ec433eee81b..c7c706c5ec6 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -3,8 +3,9 @@ process ENTREZDIRECT_ESUMMARY { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - def container_image = "/entrez-direct:16.2--he881be0_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "entrez-direct:16.2--he881be0_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), val(uid), path(uids_file) diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index b7d0d66179f..f0f3d0c4a51 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -3,8 +3,9 @@ process ENTREZDIRECT_XTRACT { label 'process_single' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) - def container_image = "/entrez-direct:16.2--he881be0_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "entrez-direct:16.2--he881be0_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(xml_input) diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index 9656a7e41ef..63ec9486044 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -3,8 +3,9 @@ process EPANG { label 'process_high' conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null) - def container_image = "/epa-ng:0.3.8--h9a82719_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "epa-ng:0.3.8--h9a82719_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(queryaln) diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index bbf15a03a3c..dfe32feed47 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -3,8 +3,9 @@ process EXPANSIONHUNTER { label 'process_low' conda (params.enable_conda ? "bioconda::expansionhunter=4.0.2" : null) - def container_image = "/expansionhunter:4.0.2--he785bd8_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "expansionhunter:4.0.2--he785bd8_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index 19b7d34caf7..a1d7288a7b3 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -3,8 +3,9 @@ process FAQCS { label 'process_medium' conda (params.enable_conda ? "bioconda::faqcs=2.10" : null) - def container_image = "/faqcs:2.10--r41h9a82719_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "faqcs:2.10--r41h9a82719_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index c2f43bd2fae..77b14aef3c4 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -4,8 +4,9 @@ process FARGENE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) - def container_image = "/fargene:0.1--py27h21c881e_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fargene:0.1--py27h21c881e_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index 4ad24730a57..fd75cde9c41 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -3,8 +3,9 @@ process FASTANI { label 'process_medium' conda (params.enable_conda ? "bioconda::fastani=1.32" : null) - def container_image = "/fastani:1.32--he1c1bb9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fastani:1.32--he1c1bb9_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(query) diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index aea224e36ae..37c3d23ac0f 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -3,8 +3,9 @@ process FASTAWINDOWS { label 'process_low' conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null) - def container_image = "/fasta_windows:0.2.4--hec16e2b_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fasta_windows:0.2.4--hec16e2b_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 3cd666089e2..e11226c2301 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -3,8 +3,9 @@ process FASTP { label 'process_medium' conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null) - def container_image = "/fastp:0.23.2--h79da9fb_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fastp:0.23.2--h79da9fb_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index f1db0764e8d..fa7787e2570 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -3,8 +3,9 @@ process FASTQC { label 'process_medium' conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - def container_image = "/fastqc:0.11.9--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fastqc:0.11.9--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index 6cbfe9dc52f..2d437465454 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -3,8 +3,9 @@ process FASTQSCAN { label 'process_low' conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null) - def container_image = "/fastq-scan:0.4.4--h7d875b9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fastq-scan:0.4.4--h7d875b9_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 85d5d224bbd..305340ca068 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -2,8 +2,9 @@ process FASTTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) - def container_image = "/fasttree:2.1.10--h516909a_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fasttree:2.1.10--h516909a_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path alignment diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 476eb2efa57..98c23a1e30a 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -3,8 +3,9 @@ process FFQ { label 'process_low' conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null) - def container_image = "/ffq:0.2.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ffq:0.2.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 21a8608d811..9ddfa9c32f0 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -3,8 +3,9 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fgbio:2.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index 84044c635d1..09a389fd8a1 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -3,8 +3,9 @@ process FGBIO_FASTQTOBAM { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fgbio:2.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 5e8d651aff2..1bcc28fcbee 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -3,8 +3,9 @@ process FGBIO_GROUPREADSBYUMI { label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fgbio:2.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(taggedbam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index 1acfbc9435f..62f1dd290be 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -3,8 +3,9 @@ process FGBIO_SORTBAM { label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fgbio:2.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 6b6839ed607..1cacdfe26bc 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -3,8 +3,9 @@ process FGBIO_ZIPPERBAMS { label 'process_single' conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null) - def container_image = "/fgbio:2.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fgbio:2.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(unmapped_bam) diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index 7f23797415f..0aa33f1aee8 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -3,8 +3,9 @@ process FILTLONG { label 'process_low' conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) - def container_image = "/filtlong:0.2.1--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "filtlong:0.2.1--h9a82719_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index f743ea592be..c13639c423f 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -2,8 +2,9 @@ process FLASH { tag "$meta.id" label 'process_medium' - def container_image = "/flash:1.2.11--hed695b0_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "flash:1.2.11--hed695b0_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 6af34bb0bbe..a307f6f199d 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -3,8 +3,9 @@ process FLYE { label 'process_high' conda (params.enable_conda ? "bioconda::flye=2.9" : null) - def container_image = "/flye:2.9--py39h6935b12_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "flye:2.9--py39h6935b12_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index a4902639366..cf17aa29c11 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -3,8 +3,9 @@ process FQ_LINT { label 'process_low' conda (params.enable_conda ? "bioconda::fq=0.9.1" : null) - def container_image = "/fq:0.9.1--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "fq:0.9.1--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 4fda2889ec8..92839ce71ac 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -3,8 +3,9 @@ process FREEBAYES { label 'process_low' conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null) - def container_image = "/freebayes:1.3.5--py38ha193a2f_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "freebayes:1.3.5--py38ha193a2f_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 00b03593f1c..b4dabfb870b 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -5,8 +5,9 @@ process GAMMA_GAMMA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gamma=2.1" : null) - def container_image = "/gamma:2.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gamma:2.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 6e2a928f008..9f20e2689fc 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -3,8 +3,9 @@ process GAPPA_EXAMINEASSIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - def container_image = "/gappa:0.8.0--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gappa:0.8.0--h9a82719_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 2d1feebbd21..82aa13f96e8 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -3,8 +3,9 @@ process GAPPA_EXAMINEGRAFT { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - def container_image = "/gappa:0.8.0--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gappa:0.8.0--h9a82719_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index bca658226d7..2f20d14174e 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -3,8 +3,9 @@ process GAPPA_EXAMINEHEATTREE { label 'process_low' conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null) - def container_image = "/gappa:0.8.0--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gappa:0.8.0--h9a82719_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index e6ae6fd0336..10bf2920306 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -3,8 +3,9 @@ process GATK_INDELREALIGNER { label 'process_single' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - def container_image = "/gatk:3.5--hdfd78af_11" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk:3.5--hdfd78af_11" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index bae7d15c9dc..821bde8c202 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -3,8 +3,9 @@ process GATK_REALIGNERTARGETCREATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - def container_image = "/gatk:3.5--hdfd78af_11" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk:3.5--hdfd78af_11" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 2c74974bac4..0e03603b4d9 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -3,8 +3,9 @@ process GATK_UNIFIEDGENOTYPER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk=3.5" : null) - def container_image = "/gatk:3.5--hdfd78af_11" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk:3.5--hdfd78af_11" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index cf49c523ac0..89460fd093b 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -3,8 +3,9 @@ process GATK4_APPLYBQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index f7f645824f1..6b2d1f138bb 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -3,8 +3,9 @@ process GATK4_APPLYVQSR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 1451b91ef45..d55030eec31 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -3,8 +3,9 @@ process GATK4_BASERECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 3482798a59b..ea26dbb6963 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -3,8 +3,9 @@ process GATK4_BEDTOINTERVALLIST { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 4a21a9633c9..ad25dfe4824 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -3,8 +3,9 @@ process GATK4_CALCULATECONTAMINATION { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 17c1a4a229d..22d4c5e087d 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -3,8 +3,9 @@ process GATK4_CALIBRATEDRAGSTRMODEL { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bam_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index aa99564a5df..eea51855c4b 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -3,8 +3,9 @@ process GATK4_COLLECTREADCOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 4872e413164..511fcd5db24 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -3,8 +3,9 @@ process GATK4_COLLECTSVEVIDENCE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 9bbe4cbc94e..45b777f2e44 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -3,8 +3,9 @@ process GATK4_COMBINEGVCFS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 12c74e8fc90..6158185c746 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -3,8 +3,9 @@ process GATK4_COMPOSESTRTABLEFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 5fc913eccca..89c4181d876 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -3,8 +3,9 @@ process GATK4_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index bdb2b490668..9fa188ed314 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -3,8 +3,9 @@ process GATK4_CREATESOMATICPANELOFNORMALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index de7a9129798..5b755ae9a55 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -3,8 +3,9 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 16f18ba5f21..275ee3f1507 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -3,8 +3,9 @@ process GATK4_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 54c95056047..c9d33d72439 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -3,8 +3,9 @@ process GATK4_FILTERMUTECTCALLS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 7747bf521b7..16b9ca2872f 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -3,8 +3,9 @@ process GATK4_FILTERVARIANTTRANCHES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index f7cd4fdd712..df18452a74b 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -3,8 +3,9 @@ process GATK4_GATHERBQSRREPORTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index a2c9221aaba..16a3e2e4e8c 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -3,8 +3,9 @@ process GATK4_GATHERPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 16c9275e778..ea469129019 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -3,8 +3,9 @@ process GATK4_GENOMICSDBIMPORT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 8172c9c911c..f66cd6c11fe 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -3,8 +3,9 @@ process GATK4_GENOTYPEGVCFS { label 'process_high' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 55654ce8cdc..a3cf517a184 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -3,8 +3,9 @@ process GATK4_GETPILEUPSUMMARIES { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 216214089f0..b3633e9ea88 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -3,8 +3,9 @@ process GATK4_HAPLOTYPECALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 50658a9d1ab..f0460e476b1 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -3,8 +3,9 @@ process GATK4_INDEXFEATUREFILE { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 1871cf32cb9..48c356e610b 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -3,8 +3,9 @@ process GATK4_INTERVALLISTTOBED { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index c2738d5fbef..882c19110ab 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -3,8 +3,9 @@ process GATK4_INTERVALLISTTOOLS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index f7ae47d5af3..4ede9cb90dc 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -3,8 +3,9 @@ process GATK4_LEARNREADORIENTATIONMODEL { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 5e398e9c1cc..cd1d40ab0ce 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -3,8 +3,9 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index a95df5d13a7..bd2eeeb29c2 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -3,8 +3,9 @@ process GATK4_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 34072eccfee..a876930ef53 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -3,8 +3,9 @@ process GATK4_MERGEBAMALIGNMENT { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 5391b9b20d5..17d7103b11b 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -3,8 +3,9 @@ process GATK4_MERGEMUTECTSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 7874740ff43..c42e2e29a4a 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -3,8 +3,9 @@ process GATK4_MERGEVCFS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index ebfcd88afcd..45aaae61abb 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -3,8 +3,9 @@ process GATK4_MUTECT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 4c479a66a04..4c7a2d4a676 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -3,8 +3,9 @@ process GATK4_PRINTSVEVIDENCE { label 'process_single' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 8faa33a416a..aa5222e7cc3 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -3,8 +3,9 @@ process GATK4_REBLOCKGVCF { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 9f12b3998fc..cd382e489f3 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -3,8 +3,9 @@ process GATK4_REVERTSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 3ca36df61fc..e851f9163b2 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -3,8 +3,9 @@ process GATK4_SAMTOFASTQ { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index a831f3bc52a..b836d6d9366 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -3,8 +3,9 @@ process GATK4_SELECTVARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index 1985cf3f107..19fa0440632 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -3,8 +3,9 @@ process GATK4_SPLITINTERVALS { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 74cf1d54cf3..df3f23c3a57 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -3,8 +3,9 @@ process GATK4_SPLITNCIGARREADS { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index ac39d31540c..1665a3d4f94 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -3,8 +3,9 @@ process GATK4_VARIANTFILTRATION { label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index ea846e1d539..37e1168061c 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -3,8 +3,9 @@ process GATK4_VARIANTRECALIBRATOR { label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) - def container_image = "/gatk4:4.2.6.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gatk4:4.2.6.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index 1d51b47fcb4..a5e9bc74fcb 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -3,8 +3,9 @@ process GECCO_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null) - def container_image = "/gecco:0.9.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gecco:0.9.2--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(hmm) diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 87c4323d747..66be4332470 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -3,8 +3,9 @@ process GENMAP_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - def container_image = "/genmap:1.3.0--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genmap:1.3.0--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index b708dac4f53..2457a90aa67 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -3,8 +3,9 @@ process GENMAP_MAPPABILITY { label 'process_high' conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null) - def container_image = "/genmap:1.3.0--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genmap:1.3.0--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index fb978ffdc97..e831a936872 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -3,8 +3,9 @@ process GENMOD_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genmod:3.7.4--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 936ad0eb567..3320c7c65be 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -3,8 +3,9 @@ process GENMOD_COMPOUND { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genmod:3.7.4--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 900fbc99349..2c64fd656ce 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -3,8 +3,9 @@ process GENMOD_MODELS { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genmod:3.7.4--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 3c11dab9eac..4f019a78d47 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -3,8 +3,9 @@ process GENMOD_SCORE { label 'process_medium' conda (params.enable_conda ? "bioconda::genmod=3.7.4" : null) - def container_image = "/genmod:3.7.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genmod:3.7.4--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index d55d4d08354..85e09760949 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -3,8 +3,9 @@ process GENOMESCOPE2 { label 'process_low' conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null) - def container_image = "/genomescope2:2.0--py310r41hdfd78af_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genomescope2:2.0--py310r41hdfd78af_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index d1ae2ab6d89..d02cf9c6ed6 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -3,8 +3,9 @@ process GENOTYPHI_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null) - def container_image = "/genotyphi:1.9.1--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genotyphi:1.9.1--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 554a5e7bc5a..240d39a2472 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -3,8 +3,9 @@ process GENRICH { label 'process_high' conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) - def container_image = "/genrich:0.6.1--h5bf99c6_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "genrich:0.6.1--h5bf99c6_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(treatment_bam) diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index 36fbed6ca3d..b6e4d018362 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -4,8 +4,9 @@ process GFAFFIX { conda (params.enable_conda ? 'bioconda::gfaffix=0.1.4' : null) - def container_image = "/gfaffix:0.1.4--hec16e2b_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gfaffix:0.1.4--hec16e2b_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index a81ac4e90ee..65b82714e8e 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -3,8 +3,9 @@ process GFFREAD { label 'process_low' conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) - def container_image = "/gffread:0.12.1--h8b12597_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gffread:0.12.1--h8b12597_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index ca1912436ac..f74aa64e014 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -3,8 +3,9 @@ process GLIMPSE_CHUNK { label 'process_medium' conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null) - def container_image = "/glimpse-bio:1.1.1--h2ce4488_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "glimpse-bio:1.1.1--h2ce4488_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 2babb3c4e20..9cce169f0cf 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -3,8 +3,9 @@ process GLNEXUS { label 'process_medium' conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null) - def container_image = "/glnexus:1.4.1--h40d77a6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "glnexus:1.4.1--h40d77a6_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index c3bfbd2ffc4..c43751e46f3 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -3,8 +3,9 @@ process GOAT_TAXONSEARCH { label 'process_single' conda (params.enable_conda ? "bioconda::goat=0.2.0" : null) - def container_image = "/goat:0.2.0--h92d785c_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "goat:0.2.0--h92d785c_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index 2855702df94..1b167b94844 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -4,8 +4,9 @@ process GRAPHMAP2_ALIGN { tag "$meta.id" conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - def container_image = "/graphmap:0.6.3--he513fc3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "graphmap:0.6.3--he513fc3_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index d1e26119469..6cec5822e8f 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -2,8 +2,9 @@ process GRAPHMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null) - def container_image = "/graphmap:0.6.3--he513fc3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "graphmap:0.6.3--he513fc3_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index 0398432537e..0bf377c9fce 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -3,8 +3,9 @@ process GSTAMA_COLLAPSE { label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - def container_image = "/gs-tama:1.0.3--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gs-tama:1.0.3--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index e4346c0c89f..542c9f1733b 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -3,8 +3,9 @@ process GSTAMA_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) - def container_image = "/gs-tama:1.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gs-tama:1.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index 76681213343..8b54a34e107 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -3,8 +3,9 @@ process GSTAMA_POLYACLEANUP { label 'process_low' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) - def container_image = "/gs-tama:1.0.3--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gs-tama:1.0.3--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 631b4dda46c..dc35a660ba3 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -4,8 +4,9 @@ process GTDBTK_CLASSIFYWF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null) - def container_image = "/gtdbtk:1.5.0--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gtdbtk:1.5.0--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path("bins/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index 9de061c768b..dfd7e24aacf 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -2,8 +2,9 @@ process GUBBINS { label 'process_medium' conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null) - def container_image = "/gubbins:3.0.0--py39h5bf99c6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gubbins:3.0.0--py39h5bf99c6_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 46769db6c03..39243699715 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -3,8 +3,9 @@ process GUNC_DOWNLOADDB { label 'process_single' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - def container_image = "/gunc:1.0.5--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gunc:1.0.5--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index b0ca3ff303b..1cd61c39fab 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -3,8 +3,9 @@ process GUNC_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null) - def container_image = "/gunc:1.0.5--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gunc:1.0.5--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index e8e440e1508..79cd51592f3 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -3,8 +3,9 @@ process GUNZIP { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: '' + container_image) } + def container_image = "ubuntu:20.04" + container [ params.container_registry ?: '' , container_image ].join('/') + input: tuple val(meta), path(archive) diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index 917c04db1ae..84f33cbf1e4 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -3,8 +3,9 @@ process GVCFTOOLS_EXTRACTVARIANTS { label 'process_low' conda (params.enable_conda ? "bioconda::gvcftools=0.17.0" : null) - def container_image = "/gvcftools:0.17.0--he941832_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "gvcftools:0.17.0--he941832_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 8b5507fa698..d8c1a738a28 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -3,8 +3,9 @@ process HAMRONIZATION_ABRICATE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hamronization:1.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index a1452c239e8..f3c59d63669 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -3,8 +3,9 @@ process HAMRONIZATION_AMRFINDERPLUS { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hamronization:1.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 552d8de6f03..7811354bcdb 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -3,8 +3,9 @@ process HAMRONIZATION_DEEPARG { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hamronization:1.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index 03ad24392c2..48f31f55f47 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -3,8 +3,9 @@ process HAMRONIZATION_FARGENE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hamronization:1.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index ed7d435636c..8360ddcadab 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -3,8 +3,9 @@ process HAMRONIZATION_RGI { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hamronization:1.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index 0b72b6a51d3..20abd42258a 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -2,8 +2,9 @@ process HAMRONIZATION_SUMMARIZE { label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) - def container_image = "/hamronization:1.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hamronization:1.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path(reports) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index c5b261f6721..3352ba56241 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -3,8 +3,9 @@ process HAPLOCHECK { label 'process_low' conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null) - def container_image = "/haplocheck:1.3.3--h4a94de4_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "haplocheck:1.3.3--h4a94de4_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index 019aa317794..e15fdc1d42d 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -3,8 +3,9 @@ process HAPLOGREP2_CLASSIFY { label 'process_low' conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null) - def container_image = "/haplogrep:2.4.0--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "haplogrep:2.4.0--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(inputfile) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index cba1118ed3e..951b0db90bf 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -4,8 +4,9 @@ process HAPPY_HAPPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hap.py:0.3.14--py27h5c5a3ab_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index d161346365f..1c8f10333af 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -4,8 +4,9 @@ process HAPPY_PREPY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null) - def container_image = "/hap.py:0.3.14--py27h5c5a3ab_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hap.py:0.3.14--py27h5c5a3ab_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(bed) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 6d2d8e9b678..7e994bfaa85 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -3,8 +3,9 @@ process HICAP { label 'process_low' conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) - def container_image = "/hicap:1.0.3--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hicap:1.0.3--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index f9fce1e2647..ada1ea9a488 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -3,8 +3,9 @@ process HIFIASM { label 'process_high' conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) - def container_image = "/hifiasm:0.15.4--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hifiasm:0.15.4--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 3979b1de579..bf5cc861745 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -4,8 +4,9 @@ process HISAT2_ALIGN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 601c1fa6ead..bf43c78c012 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -5,8 +5,9 @@ process HISAT2_BUILD { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - def container_image = "/hisat2:2.2.1--h1b792b2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hisat2:2.2.1--h1b792b2_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index caaeab906ab..0743728ab17 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -4,8 +4,9 @@ process HISAT2_EXTRACTSPLICESITES { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) - def container_image = "/hisat2:2.2.1--h1b792b2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hisat2:2.2.1--h1b792b2_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 4e436c0d761..8d9e1fc8bd2 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -3,8 +3,9 @@ process HMMCOPY_GCCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmcopy:0.1.1--h2e03b76_7" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 117b4001c83..8bef9f49ce5 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -4,8 +4,9 @@ process HMMCOPY_GENERATEMAP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmcopy:0.1.1--h2e03b76_7" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index 21de1a0b138..eeadc58cc98 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -3,8 +3,9 @@ process HMMCOPY_MAPCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmcopy:0.1.1--h2e03b76_7" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index 5e0247dfbc0..dd03d43dc34 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -4,8 +4,9 @@ process HMMCOPY_READCOUNTER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null) - def container_image = "/hmmcopy:0.1.1--h2e03b76_7" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmcopy:0.1.1--h2e03b76_7" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index bdac0bdde16..b06d96c70e2 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -3,8 +3,9 @@ process HMMER_ESLALIMASK { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmer:3.3.2--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 9a24fee96c1..5b18e8245a0 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -3,8 +3,9 @@ process HMMER_ESLREFORMAT { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmer:3.3.2--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index f1c812e83b4..3ffec25fe38 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -3,8 +3,9 @@ process HMMER_HMMALIGN { label 'process_single' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmer:3.3.2--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index ad24da5ff2f..d8ab2b89baf 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -3,8 +3,9 @@ process HMMER_HMMBUILD { label 'process_low' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h87f3376_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmer:3.3.2--h87f3376_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 3a7b2d4461f..80ac421a2f3 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -3,8 +3,9 @@ process HMMER_HMMSEARCH { label 'process_medium' conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null) - def container_image = "/hmmer:3.3.2--h1b792b2_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmmer:3.3.2--h1b792b2_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index ed1ba06903a..1a2d7a13927 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -3,8 +3,9 @@ process HMTNOTE { label 'process_low' conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null) - def container_image = "/hmtnote:0.7.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hmtnote:0.7.2--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 185a27f1903..2c9127f950a 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -4,8 +4,9 @@ process HOMER_ANNOTATEPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "homer:4.11--pl526hc9558a2_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(peak) diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index 7c5dcae4aba..ba392fffccb 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -4,8 +4,9 @@ process HOMER_FINDPEAKS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "homer:4.11--pl526hc9558a2_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 9cce134da4f..96ce3e6024b 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,8 +5,9 @@ process HOMER_MAKETAGDIRECTORY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null) - def container_image = "/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index 579377a3920..d722147035b 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -4,8 +4,9 @@ process HOMER_MAKEUCSCFILE { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "homer:4.11--pl526hc9558a2_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index 3bbc1f480f4..8c02ca1c474 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -4,8 +4,9 @@ process HOMER_POS2BED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::homer=4.11" : null) - def container_image = "/homer:4.11--pl526hc9558a2_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "homer:4.11--pl526hc9558a2_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 787d938cbab..5745568f251 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -4,8 +4,9 @@ process HPSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) - def container_image = "/hpsuissero:1.0.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hpsuissero:1.0.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index afa8a6c1132..a26dd46b7b5 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -3,8 +3,9 @@ process ICHORCNA_CREATEPON { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "r-ichorcna:0.3.2--r41hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path wigs diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index 41d79e34f50..6cbc5e61087 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -4,8 +4,9 @@ process ICHORCNA_RUN { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) - def container_image = "/r-ichorcna:0.3.2--r41hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "r-ichorcna:0.3.2--r41hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(wig) diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index bcd2df13f7f..691dba92fcc 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -3,8 +3,9 @@ process IDR { label 'process_low' conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) - def container_image = "/idr:2.0.4.2--py39hcbe4a3b_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "idr:2.0.4.2--py39hcbe4a3b_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path peaks diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index b035008f471..6b38736e1f3 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -3,8 +3,9 @@ process INSTRAIN_PROFILE { label 'process_high' conda (params.enable_conda ? "bioconda::instrain=1.6.1" : null) - def container_image = "/instrain:1.6.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "instrain:1.6.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index d77eb19bff0..cc9b128414a 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -3,8 +3,9 @@ process IQTREE { label 'process_medium' conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null) - def container_image = "/iqtree:2.1.4_beta--hdcc8f71_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "iqtree:2.1.4_beta--hdcc8f71_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path alignment diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index 4908ddbfa23..e0e2925787e 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -3,8 +3,9 @@ process ISMAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null) - def container_image = "/ismapper:2.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ismapper:2.0.2--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index 344492a6435..dd8fc614f2d 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -3,8 +3,9 @@ process ISOSEQ3_CLUSTER { label 'process_medium' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - def container_image = "/isoseq3:3.4.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "isoseq3:3.4.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index b4c2f5ababc..be98d4029a9 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -3,8 +3,9 @@ process ISOSEQ3_REFINE { label 'process_low' conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null) - def container_image = "/isoseq3:3.4.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "isoseq3:3.4.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 1021049f82e..11156bf19c0 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -3,8 +3,9 @@ process IVAR_CONSENSUS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - def container_image = "/ivar:1.3.1--h089eab3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ivar:1.3.1--h089eab3_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index c722e345cc2..c19f493a62b 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -3,8 +3,9 @@ process IVAR_TRIM { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - def container_image = "/ivar:1.3.1--h089eab3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ivar:1.3.1--h089eab3_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index c8c4b9c21ef..64d8d40d7fd 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -3,8 +3,9 @@ process IVAR_VARIANTS { label 'process_medium' conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) - def container_image = "/ivar:1.3.1--h089eab3_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ivar:1.3.1--h089eab3_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index 62ba820adff..8b3640f436c 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -8,8 +8,9 @@ process JUPYTERNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //ipykernel, jupytext, papermill and nbconvert Python packages. conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null) - def container_image = "/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index 242c1af4417..37fc9c2b943 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -3,8 +3,9 @@ process KAIJU_KAIJU { label 'process_high' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - def container_image = "/kaiju:1.8.2--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kaiju:1.8.2--h5b5514e_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 8c1cd5058af..2c848ecff07 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -3,8 +3,9 @@ process KAIJU_KAIJU2KRONA { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - def container_image = "/kaiju:1.8.2--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kaiju:1.8.2--h5b5514e_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index cec631ce376..31c7cc312db 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -3,8 +3,9 @@ process KAIJU_KAIJU2TABLE { label 'process_single' conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null) - def container_image = "/kaiju:1.8.2--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kaiju:1.8.2--h5b5514e_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(results) diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index e073cd0eca0..3c212697fea 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -3,8 +3,9 @@ process KALLISTO_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null) - def container_image = "/kallisto:0.46.2--h4f7b962_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kallisto:0.46.2--h4f7b962_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 6b1feb1b829..2282dd275c2 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -3,8 +3,9 @@ process KALLISTOBUSTOOLS_COUNT { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - def container_image = "/kb-python:0.27.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kb-python:0.27.2--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index d5a23179076..e747d524b2a 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -3,8 +3,9 @@ process KALLISTOBUSTOOLS_REF { label 'process_medium' conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null) - def container_image = "/kb-python:0.27.2--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kb-python:0.27.2--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 9cc399f5614..1fd3e6e568b 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -3,8 +3,9 @@ process KAT_HIST { label 'process_medium' conda (params.enable_conda ? "bioconda::kat=2.4.2" : null) - def container_image = "/kat:2.4.2--py38hfc5f9d8_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kat:2.4.2--py38hfc5f9d8_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index fee17545287..5f0722f5a90 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -3,8 +3,9 @@ process KHMER_NORMALIZEBYMEDIAN { label 'process_long' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - def container_image = "/khmer:3.0.0a3--py37haa7609a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "khmer:3.0.0a3--py37haa7609a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path pe_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index 8bf7d4e2bbd..ecd6e7af44e 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -3,8 +3,9 @@ process KHMER_UNIQUEKMERS { label 'process_low' conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null) - def container_image = "/khmer:3.0.0a3--py37haa7609a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "khmer:3.0.0a3--py37haa7609a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index c11de5b950a..3253fec40ab 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -3,8 +3,9 @@ process KLEBORATE { label 'process_medium' conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null) - def container_image = "/kleborate:2.1.0--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "kleborate:2.1.0--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 33501024448..2d3f2788c53 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -3,8 +3,9 @@ process KRAKEN2_KRAKEN2 { label 'process_high' conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null) - def container_image = "/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index bfc5da814a5..dbade9d9284 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,8 +2,9 @@ process KRAKENTOOLS_COMBINEKREPORTS { label 'process_single' conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - def container_image = "/krakentools:1.2--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "krakentools:1.2--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 52109a176c8..09bdf078d42 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -4,8 +4,9 @@ process KRAKENTOOLS_KREPORT2KRONA { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krakentools=1.2" : null) - def container_image = "/krakentools:1.2--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "krakentools:1.2--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index 8dd177b4808..6ec1109d451 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -4,8 +4,9 @@ process KRONA_KRONADB { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - def container_image = "/krona:2.7.1--pl526_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "krona:2.7.1--pl526_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index 23a24114281..d70f820b253 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -4,8 +4,9 @@ process KRONA_KTIMPORTTAXONOMY { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::krona=2.8" : null) - def container_image = "/krona:2.8--pl5262hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "krona:2.8--pl5262hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 042467dfb9e..64df1f0d179 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -3,8 +3,9 @@ process KRONA_KTIMPORTTEXT { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) - def container_image = "/krona:2.8.1--pl5321hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "krona:2.8.1--pl5321hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index 089f46754b0..6cb60e15341 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -4,8 +4,9 @@ process KRONA_KTUPDATETAXONOMY { label 'process_single' conda (params.enable_conda ? "bioconda::krona=2.7.1" : null) - def container_image = "/krona:2.7.1--pl526_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "krona:2.7.1--pl526_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + output: path 'taxonomy/taxonomy.tab', emit: db diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 5bd9faa068b..03487a97839 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -3,8 +3,9 @@ process LAST_DOTPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index e00910370f3..7ffe727edf1 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -3,8 +3,9 @@ process LAST_LASTAL { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index f710b02e700..925da314c9f 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -3,8 +3,9 @@ process LAST_LASTDB { label 'process_medium' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 08e3852fa17..b6332f939a5 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -3,8 +3,9 @@ process LAST_MAFCONVERT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index e125af0f4ed..0c752b103d3 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -3,8 +3,9 @@ process LAST_MAFSWAP { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 2fdcecee821..54a7b571c70 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -3,8 +3,9 @@ process LAST_POSTMASK { label 'process_low' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index 2106f2afe4b..f32b1e3a0de 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -3,8 +3,9 @@ process LAST_SPLIT { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 187be436146..da8aff592e0 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -3,8 +3,9 @@ process LAST_TRAIN { label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) - def container_image = "/last:1250--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "last:1250--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index 40b38d52cd1..24731286406 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -4,8 +4,9 @@ process LEEHOM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null) - def container_image = "/leehom:1.2.15--h29e30f7_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "leehom:1.2.15--h29e30f7_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index d5987b1a9d3..a7cd15bf781 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -3,8 +3,9 @@ process LEGSTA { label 'process_medium' conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null) - def container_image = "/legsta:0.5.1--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "legsta:0.5.1--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 2226a2050dd..8b22222965a 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -3,8 +3,9 @@ process LIMA { label 'process_low' conda (params.enable_conda ? "bioconda::lima=2.2.0" : null) - def container_image = "/lima:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "lima:2.2.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ccs) diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index f8f25ed8de4..f72b8ab3e8e 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -3,8 +3,9 @@ process LISSERO { label 'process_low' conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null) - def container_image = "/lissero:0.4.9--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "lissero:0.4.9--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index 2036fe4dfbe..a4ccf9e07ad 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -3,8 +3,9 @@ process LOFREQ_CALL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "lofreq:2.1.5--py38h588ecb2_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 8ee1ae76c6b..2f0e98078a8 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -3,8 +3,9 @@ process LOFREQ_CALLPARALLEL { label 'process_high' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "lofreq:2.1.5--py38h588ecb2_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index 32cb7988e0d..5f28a1fb2df 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -3,8 +3,9 @@ process LOFREQ_FILTER { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "lofreq:2.1.5--py38h588ecb2_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index 64a2d219355..b6562df1365 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -3,8 +3,9 @@ process LOFREQ_INDELQUAL { label 'process_low' conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null) - def container_image = "/lofreq:2.1.5--py38h588ecb2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "lofreq:2.1.5--py38h588ecb2_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index 0df58d5777f..fd79613682a 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -3,8 +3,9 @@ process MACREL_CONTIGS { label 'process_medium' conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) - def container_image = "/macrel:1.1.0--py36hc5360cc_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "macrel:1.1.0--py36hc5360cc_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 5e370924dc4..4b4e7fefd19 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -3,8 +3,9 @@ process MACS2_CALLPEAK { label 'process_medium' conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) - def container_image = "/macs2:2.2.7.1--py38h4a8c8d9_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "macs2:2.2.7.1--py38h4a8c8d9_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index aa001be3b07..7215ff4d211 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -3,8 +3,9 @@ process MAFFT { label 'process_high' conda (params.enable_conda ? "bioconda::mafft=7.490" : null) - def container_image = "/mafft:7.490--h779adbc_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mafft:7.490--h779adbc_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 93937a00747..74ab149f18f 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -3,8 +3,9 @@ process MALT_BUILD { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - def container_image = "/malt:0.41--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "malt:0.41--1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fastas diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index ec1425677c1..6e687e70f05 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -3,8 +3,9 @@ process MALT_RUN { label 'process_high' conda (params.enable_conda ? "bioconda::malt=0.41" : null) - def container_image = "/malt:0.41--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "malt:0.41--1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastqs) diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index 02ed042676b..6e3df6b4ac9 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -3,8 +3,9 @@ process MALTEXTRACT { label 'process_medium' conda (params.enable_conda ? "bioconda::hops=0.35" : null) - def container_image = "/hops:0.35--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "hops:0.35--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path rma6 diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index 0c30d771f1d..e4b7ce5e9cc 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -3,8 +3,9 @@ process MANTA_CONVERTINVERSION { label 'process_low' conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index b22fcb97c33..2b95619c986 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -3,8 +3,9 @@ process MANTA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - def container_image = "/manta:1.6.0--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "manta:1.6.0--h9ee0642_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index bbd00d11600..d68e7690d2a 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -3,8 +3,9 @@ process MANTA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - def container_image = "/manta:1.6.0--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "manta:1.6.0--h9ee0642_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 47cf68df3e1..5357f1bf8ef 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -3,8 +3,9 @@ process MANTA_TUMORONLY { label 'process_medium' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) - def container_image = "/manta:1.6.0--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "manta:1.6.0--h9ee0642_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index ca81c395f77..a462358ab6f 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -3,8 +3,9 @@ process MAPDAMAGE2 { label 'process_single' conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null) - def container_image = "/mapdamage2:2.2.1--pyr40_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mapdamage2:2.2.1--pyr40_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index 3d2d872603c..a4a48f159aa 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -3,8 +3,9 @@ process MASH_DIST { label 'process_low' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - def container_image = "/mash:2.3--he348c14_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mash:2.3--he348c14_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index 97b02c79910..ddee9832330 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -3,8 +3,9 @@ process MASH_SCREEN { label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - def container_image = "/mash:2.3--he348c14_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mash:2.3--he348c14_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(query) diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index 24515e3b9d6..d0a57e4aa92 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -2,8 +2,9 @@ process MASH_SKETCH { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::mash=2.3" : null) - def container_image = "/mash:2.3--he348c14_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mash:2.3--he348c14_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index 4ddb9f23e05..79c7c3ea797 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -3,8 +3,9 @@ process MASHTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null) - def container_image = "/mashtree:1.2.0--pl526h516909a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mashtree:1.2.0--pl526h516909a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index cdfabad70d5..03e0535ff4f 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -3,8 +3,9 @@ process MAXBIN2 { label 'process_medium' conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null) - def container_image = "/maxbin2:2.2.7--he1b5a44_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "maxbin2:2.2.7--he1b5a44_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index f0a8592a03b..b888d36b6bf 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -3,8 +3,9 @@ process MAXQUANT_LFQ { label 'process_long' conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null) - def container_image = "/maxquant:2.0.3.0--py310hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "maxquant:2.0.3.0--py310hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta), path(paramfile) diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index aa36e56a765..0ec3a103a6c 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -4,8 +4,9 @@ process MCRONI { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null) - def container_image = "/mcroni:1.0.4--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mcroni:1.0.4--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index 0f95fb8fbd8..4df7bbe5d2b 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -3,8 +3,9 @@ process MD5SUM { label 'process_single' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: '' + container_image) } + def container_image = "ubuntu:20.04" + container [ params.container_registry ?: '' , container_image ].join('/') + input: tuple val(meta), path(file) diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index bf42c9b845a..dbbefd65bad 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -3,8 +3,9 @@ process MEDAKA { label 'process_high' conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) - def container_image = "/medaka:1.4.4--py38h130def0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "medaka:1.4.4--py38h130def0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 3692eaacd6a..2e5f03d5986 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -3,8 +3,9 @@ process MEGAHIT { label 'process_high' conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null) - def container_image = "/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index 08269dabce0..6fef5a26d30 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -3,8 +3,9 @@ process MEGAN_DAA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - def container_image = "/megan:6.21.7--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "megan:6.21.7--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(daa) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index a977bd65ac1..66b9ae81544 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -3,8 +3,9 @@ process MEGAN_RMA2INFO { label 'process_single' conda (params.enable_conda ? "bioconda::megan=6.21.7" : null) - def container_image = "/megan:6.21.7--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "megan:6.21.7--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index 75d81ff2406..2f3cb3f3825 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -3,8 +3,9 @@ process MENINGOTYPE { label 'process_low' conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) - def container_image = "/meningotype:0.8.5--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "meningotype:0.8.5--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index b9eb1a8de4e..89bd6d3e6fe 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -3,8 +3,9 @@ process MERQURY { label 'process_low' conda (params.enable_conda ? "bioconda::merqury=1.3" : null) - def container_image = "/merqury:1.3--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "merqury:1.3--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index b7f72b49304..c24f8e26c9d 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -3,8 +3,9 @@ process MERYL_COUNT { label 'process_medium' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - def container_image = "/meryl:1.3--h87f3376_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "meryl:1.3--h87f3376_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 8d6de50f91c..11a717bd140 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -3,8 +3,9 @@ process MERYL_HISTOGRAM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - def container_image = "/meryl:1.3--h87f3376_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "meryl:1.3--h87f3376_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 9e2b0dfeacd..d10255a1478 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -3,8 +3,9 @@ process MERYL_UNIONSUM { label 'process_low' conda (params.enable_conda ? "bioconda::meryl=1.3" : null) - def container_image = "/meryl:1.3--h87f3376_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "meryl:1.3--h87f3376_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 6daec895952..2bd8c8b253d 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -3,8 +3,9 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - def container_image = "/metabat2:2.15--h986a166_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "metabat2:2.15--h986a166_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 8318eda35e2..0af0fe49d5b 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -3,8 +3,9 @@ process METABAT2_METABAT2 { label 'process_medium' conda (params.enable_conda ? "bioconda::metabat2=2.15" : null) - def container_image = "/metabat2:2.15--h986a166_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "metabat2:2.15--h986a166_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index a333e6a776c..e957c150ba1 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,8 +2,9 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { label 'process_single' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "metaphlan:3.0.12--pyhb7b1952_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index 505d24ff48d..b42f8b39fa2 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -3,8 +3,9 @@ process METAPHLAN3_METAPHLAN3 { label 'process_high' conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null) - def container_image = "/metaphlan:3.0.12--pyhb7b1952_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "metaphlan:3.0.12--pyhb7b1952_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 1a762880673..91e8a9d20c5 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -3,8 +3,9 @@ process METHYLDACKEL_EXTRACT { label 'process_medium' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - def container_image = "/methyldackel:0.6.0--h22771d5_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "methyldackel:0.6.0--h22771d5_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index 7ba33944c62..ed696aa08e5 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -3,8 +3,9 @@ process METHYLDACKEL_MBIAS { label 'process_low' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) - def container_image = "/methyldackel:0.6.0--h22771d5_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "methyldackel:0.6.0--h22771d5_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index cb5b6df306d..ee85602992e 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -3,8 +3,9 @@ process MINIA { label 'process_high' conda (params.enable_conda ? "bioconda::minia=3.2.6" : null) - def container_image = "/minia:3.2.6--h9a82719_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "minia:3.2.6--h9a82719_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index cfff80b718e..61b9cdff5d5 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -3,8 +3,9 @@ process MINIASM { label 'process_high' conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) - def container_image = "/miniasm:0.3_r179--h5bf99c6_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "miniasm:0.3_r179--h5bf99c6_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index ddd1d2fe61d..c776418349c 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -3,8 +3,9 @@ process MINIMAP2_ALIGN { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) - def container_image = "/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 955eb0da515..508cb37877f 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -2,8 +2,9 @@ process MINIMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) - def container_image = "/minimap2:2.21--h5bf99c6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "minimap2:2.21--h5bf99c6_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 0d728c4a750..7f20592503e 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -3,8 +3,9 @@ process MLST { label 'process_low' conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) - def container_image = "/mlst:2.19.0--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mlst:2.19.0--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index 051889f006d..844e5d3d292 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -3,8 +3,9 @@ process MOBSUITE_RECON { label 'process_medium' conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null) - def container_image = "/mob_suite:3.0.3--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mob_suite:3.0.3--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index fe54ed4453d..32e8478630d 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -3,8 +3,9 @@ process MOSDEPTH { label 'process_medium' conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) - def container_image = "/mosdepth:0.3.3--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mosdepth:0.3.3--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index e459d3e8311..1ecc14be703 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -2,8 +2,9 @@ process MOTUS_DOWNLOADDB { label 'process_low' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - def container_image = "/motus:3.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "motus:3.0.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 17e5fb35f14..5d8f7911542 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -5,8 +5,9 @@ process MOTUS_MERGE { label 'process_single' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - def container_image = "/motus:3.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "motus:3.0.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index e3554e1ce3e..c9e02852ba6 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -3,8 +3,9 @@ process MOTUS_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::motus=3.0.1" : null) - def container_image = "/motus:3.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "motus:3.0.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index ce8734fc98a..0c4964aed62 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -3,8 +3,9 @@ process MSISENSOR_MSI { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - def container_image = "/msisensor:0.5--hb3646a4_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "msisensor:0.5--hb3646a4_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index ce6dd3eac7c..3c996075cf7 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -3,8 +3,9 @@ process MSISENSOR_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor=0.5" : null) - def container_image = "/msisensor:0.5--hb3646a4_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "msisensor:0.5--hb3646a4_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index c55313c3700..355cf3f43ae 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -3,8 +3,9 @@ process MSISENSOR2_MSI { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - def container_image = "/msisensor2:0.1--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "msisensor2:0.1--hd03093a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index a9a5e413ce6..c91e35ee1aa 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -3,8 +3,9 @@ process MSISENSOR2_SCAN { label 'process_medium' conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null) - def container_image = "/msisensor2:0.1--hd03093a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "msisensor2:0.1--hd03093a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index 85531a75783..45dbf2dc90b 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -3,8 +3,9 @@ process MSISENSORPRO_MSI_SOMATIC { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "msisensor-pro:1.2.0--hfc31af2_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index f60a31e36e0..a6cd3dde079 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -3,8 +3,9 @@ process MSISENSORPRO_SCAN { label 'process_low' conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) - def container_image = "/msisensor-pro:1.2.0--hfc31af2_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "msisensor-pro:1.2.0--hfc31af2_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index 9ed6a7e42b5..c71f21da3f4 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -3,8 +3,9 @@ process MTNUCRATIO { label 'process_single' conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) - def container_image = "/mtnucratio:0.7--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mtnucratio:0.7--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 7dd8515874c..0a0d618c196 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -2,8 +2,9 @@ process MULTIQC { label 'process_single' conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) - def container_image = "/multiqc:1.13--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "multiqc:1.13--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 648947ce10a..74aa3fd9059 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -3,8 +3,9 @@ process MULTIVCFANALYZER { label 'process_single' conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null) - def container_image = "/multivcfanalyzer:0.85.2--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "multivcfanalyzer:0.85.2--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path vcfs diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index c1fa75e8f86..9928e269656 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -4,8 +4,9 @@ process MUMMER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - def container_image = "/mummer:3.23--pl5262h1b792b2_12" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mummer:3.23--pl5262h1b792b2_12" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index d41467933b5..0e51ab58ef2 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -3,8 +3,9 @@ process MUSCLE { label 'process_single' conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) - def container_image = "/muscle:3.8.1551--h7d875b9_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "muscle:3.8.1551--h7d875b9_6" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index 38316f80a68..f15177b8577 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -3,8 +3,9 @@ process MYKROBE_PREDICT { label 'process_low' conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null) - def container_image = "/mykrobe:0.11.0--py39h2add14b_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mykrobe:0.11.0--py39h2add14b_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index 9045fc60be9..ccc17c52ff8 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -3,8 +3,9 @@ process NANOLYSE { label 'process_low' conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) - def container_image = "/nanolyse:1.2.0--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "nanolyse:1.2.0--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index ad7d30ca7da..4c7356547f5 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -3,8 +3,9 @@ process NANOPLOT { label 'process_low' conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null) - def container_image = "/nanoplot:1.40.0--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "nanoplot:1.40.0--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index 69539b07204..e3819ab2ab1 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -3,8 +3,9 @@ process NCBIGENOMEDOWNLOAD { label 'process_low' conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.1" : null) - def container_image = "/ncbi-genome-download:0.3.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ncbi-genome-download:0.3.1--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: val meta diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index cb9d0e58f87..22e89d55591 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -3,8 +3,9 @@ process NEXTCLADE_DATASETGET { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - def container_image = "/nextclade:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "nextclade:2.2.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 7ef8f630cb7..70e06df09e6 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -3,8 +3,9 @@ process NEXTCLADE_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null) - def container_image = "/nextclade:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "nextclade:2.2.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index 50ff5164c1a..c3ba5174675 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -3,8 +3,9 @@ process NEXTGENMAP { label 'process_medium' conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null) - def container_image = "/nextgenmap:0.5.5--hc9558a2_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "nextgenmap:0.5.5--hc9558a2_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index 08d96c13ec5..602acaaa5fe 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -3,8 +3,9 @@ process NGMASTER { label 'process_low' conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null) - def container_image = "/ngmaster:0.5.8--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ngmaster:0.5.8--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index b814d8836ca..92fe2e82811 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,8 +2,9 @@ process NGSCHECKMATE_NCM { label 'process_low' conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) - def container_image = "/ngscheckmate:1.0.0--py27r41hdfd78af_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ngscheckmate:1.0.0--py27r41hdfd78af_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path files diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index 3844fd95f1c..d58b778bb7f 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -3,8 +3,9 @@ process NUCMER { label 'process_low' conda (params.enable_conda ? "bioconda::mummer=3.23" : null) - def container_image = "/mummer:3.23--pl5262h1b792b2_12" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mummer:3.23--pl5262h1b792b2_12" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 68db773c69c..0a9c1f6d01e 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -3,8 +3,9 @@ process OPTITYPE { label 'process_medium' conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null) - def container_image = "/optitype:1.3.5--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "optitype:1.3.5--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index 59150c677fe..fed85537015 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -3,8 +3,9 @@ process PAIRIX { label 'process_medium' conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null) - def container_image = "/pairix:0.3.7--py36h30a8e3e_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairix:0.3.7--py36h30a8e3e_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index b782a287d79..8c3022cf059 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_DEDUP { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 1b686db3c9d..9054298c8cb 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_FLIP { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(sam) diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 33c8d73f106..46b9e4a0f2b 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_PARSE { label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 7b4211a899e..9540d3fff50 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_RESTRICT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pairs) diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index ec00eddd00f..7a2f82c2125 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_SELECT { label 'process_medium' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index cb4ffcdf184..e72449056b0 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -3,8 +3,9 @@ process PAIRTOOLS_SORT { label 'process_high' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) - def container_image = "/pairtools:0.3.0--py37hb9c2fc3_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index f892bff44f4..a85e7bb16c5 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -3,8 +3,9 @@ process PANAROO_RUN { label 'process_medium' conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null) - def container_image = "/panaroo:1.2.9--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "panaroo:1.2.9--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 7f92744ba16..6ec4ce64f9c 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -3,8 +3,9 @@ process PANGOLIN { label 'process_medium' conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null) - def container_image = "/pangolin:4.1.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pangolin:4.1.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index ad1161e55a4..52bc42d47b0 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -4,8 +4,9 @@ process PARACLU { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::paraclu=10" : null) - def container_image = "/paraclu:10--h9a82719_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "paraclu:10--h9a82719_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index d2fb8736b58..445c022bd71 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -3,8 +3,9 @@ process PASTY { label 'process_single' conda (params.enable_conda ? "bioconda::pasty=1.0.0" : null) - def container_image = "/pasty:1.0.0--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pasty:1.0.0--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index 7fd452dd425..98d6d02c4b1 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -3,8 +3,9 @@ process PBBAM_PBMERGE { label 'process_low' conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) - def container_image = "/pbbam:1.7.0--h058f120_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pbbam:1.7.0--h058f120_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 47e12094a59..1dc2f20cae4 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -3,8 +3,9 @@ process PBCCS { label 'process_low' conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null) - def container_image = "/pbccs:6.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pbccs:6.2.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(pbi) diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 745aaca77c8..05896d2afbe 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -3,8 +3,9 @@ process PBPTYPER { label 'process_single' conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null) - def container_image = "/pbptyper:1.0.2--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pbptyper:1.0.2--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index 45b9db5929d..7c1666f2b8a 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -3,8 +3,9 @@ process PEAR { label 'process_low' conda (params.enable_conda ? "bioconda::pear=0.9.6" : null) - def container_image = "/pear:0.9.6--h67092d7_8" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pear:0.9.6--h67092d7_8" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index e70c88cd8e8..dca940a4e14 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -3,8 +3,9 @@ process PEDDY { label 'process_low' conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null) - def container_image = "/peddy:0.4.8--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "peddy:0.4.8--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 89b046cf1d8..11cd707a68c 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -4,8 +4,9 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) - def container_image = "/phantompeakqualtools:1.2.2--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "phantompeakqualtools:1.2.2--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index ccc9b62d3fe..c1a520e80d9 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -3,8 +3,9 @@ process PHYLOFLASH { label 'process_medium' conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null) - def container_image = "/phyloflash:3.4--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "phyloflash:3.4--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 42103a93f3c..60e514a2d6a 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -3,8 +3,9 @@ process PICARD_ADDORREPLACEREADGROUPS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 3f756092fae..10626eef9eb 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -3,8 +3,9 @@ process PICARD_CLEANSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 328cca815e5..d9d92b235f9 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -3,8 +3,9 @@ process PICARD_COLLECTHSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 9834b697db3..4ff2098c587 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -3,8 +3,9 @@ process PICARD_COLLECTMULTIPLEMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index bab23c6d5c7..e2a46ebe263 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -3,8 +3,9 @@ process PICARD_COLLECTWGSMETRICS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 8ebfa337728..87efe40f8a0 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -3,8 +3,9 @@ process PICARD_CREATESEQUENCEDICTIONARY { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index 97265ef2147..bb3d94a9a94 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -3,8 +3,9 @@ process PICARD_CROSSCHECKFINGERPRINTS { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input1) diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index 8ca715f6990..46be4ee0954 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -3,8 +3,9 @@ process PICARD_FASTQTOSAM { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index c2ed6354b0f..a446dcbbfdd 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -3,8 +3,9 @@ process PICARD_FILTERSAMREADS { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index e173fa8a330..9080f74fe68 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -3,8 +3,9 @@ process PICARD_FIXMATEINFORMATION { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 95bcc090602..51189ba1954 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -3,8 +3,9 @@ process PICARD_LIFTOVERVCF { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index ae01fcf6e82..493f4b13375 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -3,8 +3,9 @@ process PICARD_MARKDUPLICATES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 6390fd687ae..3e3b6120a09 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -3,8 +3,9 @@ process PICARD_MERGESAMFILES { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index b26d6630447..782ac3dbd7a 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -4,8 +4,9 @@ process PICARD_RENAMESAMPLEINVCF { label 'process_single' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index e2288e15e5f..b9765c26ace 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -3,8 +3,9 @@ process PICARD_SORTSAM { label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 1a7aba1bfa2..463f9d24cbc 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -3,8 +3,9 @@ process PICARD_SORTVCF { label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) - def container_image = "/picard:2.27.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "picard:2.27.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index 0cdd2e4d9de..70d04cf42a5 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -3,8 +3,9 @@ process PINTS_CALLER { label 'process_medium' conda (params.enable_conda ? "bioconda::pypints=1.1.6" : null) - def container_image = "/pypints:1.1.6--pyh5e36f6f_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pypints:1.1.6--pyh5e36f6f_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index 7628016a3f0..c32dae56270 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -3,8 +3,9 @@ process PIRATE { label 'process_medium' conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null) - def container_image = "/pirate:1.0.4--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pirate:1.0.4--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index c99139a9077..4436fe30bd8 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -4,8 +4,9 @@ process PLASMIDFINDER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null) - def container_image = "/plasmidfinder:2.1.6--py310hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plasmidfinder:2.1.6--py310hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index c3cf0219077..c85d57c2fef 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -3,8 +3,9 @@ process PLASMIDID { label 'process_medium' conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null) - def container_image = "/plasmidid:1.6.5--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plasmidid:1.6.5--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index 39ff25c52d3..5ba39535625 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -3,8 +3,9 @@ process PLINK_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - def container_image = "/plink:1.90b6.21--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plink:1.90b6.21--h779adbc_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index b0848c46850..a8d80a7ff2f 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -3,8 +3,9 @@ process PLINK_VCF { label 'process_medium' conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null) - def container_image = "/plink:1.90b6.21--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plink:1.90b6.21--h779adbc_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index bb3f4d43560..60d2e53502e 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -3,8 +3,9 @@ process PLINK2_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - def container_image = "/plink2:2.00a2.3--h712d239_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plink2:2.00a2.3--h712d239_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index 82fe2d3879a..be2a2dc30d7 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -3,8 +3,9 @@ process PLINK2_SCORE { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - def container_image = "/plink2:2.00a2.3--h712d239_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plink2:2.00a2.3--h712d239_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(pgen), path(psam), path(pvar) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index 852ffabb14a..f9bd89729f0 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -3,8 +3,9 @@ process PLINK2_VCF { label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) - def container_image = "/plink2:2.00a2.3--h712d239_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "plink2:2.00a2.3--h712d239_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index 88bcaf2abee..a685e7bf257 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -3,8 +3,9 @@ process PMDTOOLS_FILTER { label 'process_medium' conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null) - def container_image = "/pmdtools:0.60--hdfd78af_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pmdtools:0.60--hdfd78af_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path (bai) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index db6ec83efd1..e911e2d7d33 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -3,8 +3,9 @@ process PORECHOP { label 'process_medium' conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) - def container_image = "/porechop:0.2.4--py39h7cff6ad_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "porechop:0.2.4--py39h7cff6ad_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 8cb57b9b82b..6d9558765e3 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -4,8 +4,9 @@ process PRESEQ_CCURVE { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - def container_image = "/preseq:3.1.2--h445547b_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "preseq:3.1.2--h445547b_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 808da135299..eb748dd8631 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -4,8 +4,9 @@ process PRESEQ_LCEXTRAP { label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) - def container_image = "/preseq:3.1.2--h445547b_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "preseq:3.1.2--h445547b_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index 862e6b29862..d805cc590a5 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -3,8 +3,9 @@ process PRINSEQPLUSPLUS { label 'process_low' conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null) - def container_image = "/prinseq-plus-plus:1.2.3--hc90279e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "prinseq-plus-plus:1.2.3--hc90279e_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 0ce6cd3b8f5..b9393612ed7 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -3,8 +3,9 @@ process PRODIGAL { label 'process_single' conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null) - def container_image = "/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(genome) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index d0624957928..108bb4559f7 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -3,8 +3,9 @@ process PROKKA { label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) - def container_image = "/prokka:1.14.6--pl5321hdfd78af_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "prokka:1.14.6--pl5321hdfd78af_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index e28f13c1f8d..5a7543a2fd5 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -3,8 +3,9 @@ process PYCOQC { label 'process_medium' conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null) - def container_image = "/pycoqc:2.5.2--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pycoqc:2.5.2--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index 359f1f42828..610d8c6a798 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -3,8 +3,9 @@ process PYDAMAGE_ANALYZE { label 'process_medium' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - def container_image = "/pydamage:0.70--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pydamage:0.70--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index 231f2b7b2ca..b2938e40e9a 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -3,8 +3,9 @@ process PYDAMAGE_FILTER { label 'process_single' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) - def container_image = "/pydamage:0.70--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "pydamage:0.70--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index 39e0bce88fc..cac598a662c 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -3,8 +3,9 @@ process QCAT { label 'process_medium' conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null) - def container_image = "/qcat:1.1.0--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "qcat:1.1.0--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 6babc701872..95ece0f93b0 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -3,8 +3,9 @@ process QUALIMAP_BAMQC { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - def container_image = "/qualimap:2.2.2d--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "qualimap:2.2.2d--1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index fef20f20fc8..3ba2ac404be 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -3,8 +3,9 @@ process QUALIMAP_BAMQCCRAM { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(cram), path(crai) diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 128eed9acdd..0b4e1fc5432 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -3,8 +3,9 @@ process QUALIMAP_RNASEQ { label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) - def container_image = "/qualimap:2.2.2d--1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "qualimap:2.2.2d--1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index 27a127b39f8..26e46f960ca 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -2,8 +2,9 @@ process QUAST { label 'process_medium' conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null) - def container_image = "/quast:5.2.0--py39pl5321h2add14b_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "quast:5.2.0--py39pl5321h2add14b_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path consensus diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index b5ded55141f..fbdee3c4bb7 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -3,8 +3,9 @@ process RACON { label 'process_high' conda (params.enable_conda ? "bioconda::racon=1.4.20" : null) - def container_image = "/racon:1.4.20--h9a82719_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "racon:1.4.20--h9a82719_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index b03045aac59..81fcbe9b12e 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -3,8 +3,9 @@ process RAPIDNJ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) - def container_image = "/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index 8f9c5130b7b..aa76407633c 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -3,8 +3,9 @@ process RASUSA { label 'process_low' conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null) - def container_image = "/rasusa:0.3.0--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rasusa:0.3.0--h779adbc_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads), val(genome_size) diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index 3baae4df403..37d216f887f 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -3,8 +3,9 @@ process RAVEN { label 'process_medium' conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null) - def container_image = "/raven-assembler:1.6.1--h2e03b76_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "raven-assembler:1.6.1--h2e03b76_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index c950c45b728..890e986f7f4 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -2,8 +2,9 @@ process RAXMLNG { label 'process_high' conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null) - def container_image = "/raxml-ng:1.0.3--h32fcf60_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "raxml-ng:1.0.3--h32fcf60_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 763d8ae2c2e..d2f0e2997be 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -3,8 +3,9 @@ process RGI_MAIN { label 'process_medium' conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) - def container_image = "/rgi:5.2.1--pyha8f3691_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rgi:5.2.1--pyha8f3691_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 76f71718a41..15d10476d77 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -3,8 +3,9 @@ process RHOCALL_ANNOTATE { label 'process_medium' conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null) - def container_image = "/rhocall:0.5.1--py39hbf8eff0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rhocall:0.5.1--py39hbf8eff0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 7753f61fa0e..1dc9f3262e0 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -8,8 +8,9 @@ process RMARKDOWNNOTEBOOK { //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null) - def container_image = "/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" + container [ params.container_registry ?: 'quay.io/biocontainers' ,container_image ].join('/') + input: tuple val(meta), path(notebook) diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index 1eec1d9f8e3..b13dda41636 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -3,8 +3,9 @@ process ROARY { label 'process_medium' conda (params.enable_conda ? "bioconda::roary=3.13.0" : null) - def container_image = "/roary:3.13.0--pl526h516909a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "roary:3.13.0--pl526h516909a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index d0dfc33585c..de3b15c983c 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -3,8 +3,9 @@ process RSEM_CALCULATEEXPRESSION { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index fde8eb88ed6..2b2a0947a6e 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -3,8 +3,9 @@ process RSEM_PREPAREREFERENCE { label 'process_high' conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null) - def container_image = "/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta, stageAs: "rsem/*" diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index e27f11bbb4d..753b5f33540 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -3,8 +3,9 @@ process RSEQC_BAMSTAT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index c401c2fc3e7..8f4bffabfcb 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -3,8 +3,9 @@ process RSEQC_INFEREXPERIMENT { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index 40fb8331eab..05c071b628b 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -3,8 +3,9 @@ process RSEQC_INNERDISTANCE { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index e3e50b4b5ba..9bb71510d7a 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -3,8 +3,9 @@ process RSEQC_JUNCTIONANNOTATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 382a7a59cde..38e38b96dcf 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -3,8 +3,9 @@ process RSEQC_JUNCTIONSATURATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index 3c7ef15271c..f3ad940aeb7 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -3,8 +3,9 @@ process RSEQC_READDISTRIBUTION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index b8fcacc86d5..22c1824dc0c 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -3,8 +3,9 @@ process RSEQC_READDUPLICATION { label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 645b165f239..aa5f9cf9181 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -3,8 +3,9 @@ process RSEQC_TIN { label 'process_high' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) - def container_image = "/rseqc:3.0.1--py37h516909a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rseqc:3.0.1--py37h516909a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 6024b164b7b..8f9bdc1b1d6 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -3,8 +3,9 @@ process RTGTOOLS_PEDFILTER { label 'process_low' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - def container_image = "/rtg-tools:3.12.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rtg-tools:3.12.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 2eac07bb63a..18b0bbf3d76 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -3,8 +3,9 @@ process RTGTOOLS_VCFEVAL { label 'process_medium' conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) - def container_image = "/rtg-tools:3.12.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "rtg-tools:3.12.1--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index f7efcf6144c..70e1329ed44 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -3,8 +3,9 @@ process SALMON_INDEX { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - def container_image = "/salmon:1.5.2--h84f40af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "salmon:1.5.2--h84f40af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path genome_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 7d48f97dedb..75183bb1b7b 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -3,8 +3,9 @@ process SALMON_QUANT { label "process_medium" conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null) - def container_image = "/salmon:1.5.2--h84f40af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "salmon:1.5.2--h84f40af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index 736ea1f879e..b4136e0c233 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -3,8 +3,9 @@ process SAMBLASTER { label 'process_low' conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 9075c9252f5..8fe142c3614 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_AMPLICONCLIP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index e251d6dd268..efd5eaa03a6 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_BAM2FQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index c2ad471d591..c934fd9deac 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_COLLATE { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 2c2997cc676..1bce458c081 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_COLLATEFASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 5a435765887..97ad0ef5044 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_CONVERT { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 74c4a313b1a..1fa97e00efd 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_DEPTH { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 6b27f658a80..a58aa52e80e 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_DICT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 9f3d2de1138..acc5259fb68 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_FAIDX { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 798f4e66250..5229908e7d3 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_FASTA { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 65e755be9ee..3768d17b369 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_FASTQ { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 4a4b4271a27..8a05bf265f0 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_FIXMATE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index e6a6dfb66fc..472c861d435 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_FLAGSTAT { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index f98c9b5f928..17d2fae5d04 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_GETRG { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 2aabfe8e69d..4960a684009 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_IDXSTATS { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index d20b72da0ad..adbb8a19eae 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 5483ae11867..5f73dd24fa3 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_MARKDUP { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 979bcf0b834..acb665d461c 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_MERGE { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index 47ecd071026..19be610036a 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_MPILEUP { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index c12227f1255..485c8d15a4f 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_SORT { label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 3e4c2c877b9..396ba12967d 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_STATS { label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 603f9ad8a4d..dfb8262e0be 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -3,8 +3,9 @@ process SAMTOOLS_VIEW { label 'process_low' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) - def container_image = "/samtools:1.15.1--h1170115_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "samtools:1.15.1--h1170115_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index 9ec2a767f29..c073b484f48 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -3,8 +3,9 @@ process SCOARY { label 'process_low' conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null) - def container_image = "/scoary:1.6.16--py_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "scoary:1.6.16--py_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(genes), path(traits) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index 7d3dd518e1c..a734f808d4b 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -3,8 +3,9 @@ process SCRAMBLE_CLUSTERANALYSIS { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - def container_image = "/scramble:1.0.1--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "scramble:1.0.1--h779adbc_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(clusters) diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index e5bc472d659..23bd7b493b3 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -3,8 +3,9 @@ process SCRAMBLE_CLUSTERIDENTIFIER { label 'process_single' conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null) - def container_image = "/scramble:1.0.1--h779adbc_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "scramble:1.0.1--h779adbc_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index f1987432015..625b807bf45 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -4,8 +4,9 @@ process SEACR_CALLPEAK { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null) - def container_image = "/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index a83a5f97732..4e2c829fa1e 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -3,8 +3,9 @@ process SEQKIT_PAIR { label 'process_medium' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - def container_image = "/seqkit:2.1.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqkit:2.1.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index 6944c42312d..d6fbad78151 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -3,8 +3,9 @@ process SEQKIT_REPLACE { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) - def container_image = "/seqkit:2.1.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqkit:2.1.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index 4e05035e5a6..af4c335b26b 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -3,8 +3,9 @@ process SEQKIT_SPLIT2 { label 'process_medium' conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null) - def container_image = "/seqkit:2.1.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqkit:2.1.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index e7956607b1b..1085f896b93 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -3,8 +3,9 @@ process SEQKIT_STATS { label 'process_low' conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) - def container_image = "/seqkit:2.2.0--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqkit:2.2.0--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index 060cb50a05b..c8a58ae3331 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -3,8 +3,9 @@ process SEQSERO2 { label 'process_low' conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) - def container_image = "/seqsero2:1.2.1--py_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqsero2:1.2.1--py_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 9edeb97784a..772e439ea81 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -3,8 +3,9 @@ process SEQTK_MERGEPE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqtk:1.3--h5bf99c6_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index 62814a8e198..140fab18cb5 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -3,8 +3,9 @@ process SEQTK_RENAME { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqtk:1.3--h5bf99c6_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index 2c114b44e28..a71ab5a49d2 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -3,8 +3,9 @@ process SEQTK_SAMPLE { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqtk:1.3--h5bf99c6_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 209229cf461..45fe7c3b519 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -3,8 +3,9 @@ process SEQTK_SEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqtk:1.3--h5bf99c6_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 3c38cdd3b86..93d4e6e0432 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -3,8 +3,9 @@ process SEQTK_SUBSEQ { label 'process_single' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) - def container_image = "/seqtk:1.3--h5bf99c6_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqtk:1.3--h5bf99c6_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path sequences diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index a1a93ca19b1..163cfe392c3 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -3,8 +3,9 @@ process SEQUENZAUTILS_BAM2SEQZ { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sequenza-utils:3.0.0--py38h6ed170a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(normalbam), path(tumourbam) diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 284c8a4f311..55861616b9e 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -3,8 +3,9 @@ process SEQUENZAUTILS_GCWIGGLE { label 'process_medium' conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null) - def container_image = "/sequenza-utils:3.0.0--py38h6ed170a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sequenza-utils:3.0.0--py38h6ed170a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 38c82e1f932..1243a72b707 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -4,8 +4,9 @@ process SEQWISH_INDUCE { conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null) - def container_image = "/seqwish:0.7.6--h5b5514e_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seqwish:0.7.6--h5b5514e_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 600218f1e4b..2dc46c14a06 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -3,8 +3,9 @@ process SEROBA_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null) - def container_image = "/seroba:1.0.2--pyhdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "seroba:1.0.2--pyhdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index f80c4562ec1..21a73e61110 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -3,8 +3,9 @@ process SEXDETERRMINE { label 'process_single' conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null) - def container_image = "/sexdeterrmine:1.1.2--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sexdeterrmine:1.1.2--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(depth) diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 4bbb9a729e7..4e9ef63d788 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -3,8 +3,9 @@ process SHASTA { label 'process_medium' conda (params.enable_conda ? "bioconda::shasta=0.8.0" : null) - def container_image = "/shasta:0.8.0--h7d875b9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "shasta:0.8.0--h7d875b9_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index 58510c76a07..a2510e4b9a1 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -3,8 +3,9 @@ process SHASUM { label 'process_low' conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null) - def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: '' + container_image) } + def container_image = "ubuntu:20.04" + container [ params.container_registry ?: '' , container_image ].join('/') + input: tuple val(meta), path(file) diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index aa94cd77a66..4aa7c76ebbd 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -3,8 +3,9 @@ process SHIGATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null) - def container_image = "/shigatyper:2.0.1--pyhdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "shigatyper:2.0.1--pyhdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index cb66f702a0e..1f7d25e28d5 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -3,8 +3,9 @@ process SHOVILL { label 'process_medium' conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null) - def container_image = "/shovill:1.1.0--0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "shovill:1.1.0--0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 84d856b3001..42eadc47c5f 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -3,8 +3,9 @@ process SISTR { label 'process_medium' conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) - def container_image = "/sistr_cmd:1.1.1--pyh864c0ab_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sistr_cmd:1.1.1--pyh864c0ab_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 9eb8de25d6e..835fb7da508 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -4,8 +4,9 @@ process SLIMFASTQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null) - def container_image = "/slimfastq:2.04--h87f3376_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "slimfastq:2.04--h87f3376_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index 2ddafcda8c5..fc5d0895625 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -3,8 +3,9 @@ process SNAPALIGNER_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - def container_image = "/snap-aligner:2.0.1--hd03093a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snap-aligner:2.0.1--hd03093a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index 69997b23acf..877122911af 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -3,8 +3,9 @@ process SNAPALIGNER_INDEX { label 'process_high' conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null) - def container_image = "/snap-aligner:2.0.1--hd03093a_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snap-aligner:2.0.1--hd03093a_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index 0a04679a307..669e5c68da0 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -3,8 +3,9 @@ process SNIPPY_CORE { label 'process_medium' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - def container_image = "/snippy:4.6.0--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snippy:4.6.0--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(aligned_fa) diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index d1055362d51..9abe5dbe634 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -3,8 +3,9 @@ process SNIPPY_RUN { label 'process_low' conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null) - def container_image = "/snippy:4.6.0--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snippy:4.6.0--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 7528cf6c432..6d450ddf230 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -3,8 +3,9 @@ process SNPDISTS { label 'process_low' conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null) - def container_image = "/snp-dists:0.8.2--h5bf99c6_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snp-dists:0.8.2--h5bf99c6_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index 730fb9b3b1f..ebe7006c536 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -3,8 +3,9 @@ process SNPEFF { label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.1" : null) - def container_image = "/snpeff:5.1--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snpeff:5.1--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index ab1b1125190..d5a8e037e85 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -3,8 +3,9 @@ process SNPSIFT_SPLIT { label 'process_low' conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) - def container_image = "/snpsift:4.3.1t--hdfd78af_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snpsift:4.3.1t--hdfd78af_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index 905da8b0fc3..7557130b292 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -2,8 +2,9 @@ process SNPSITES { label 'process_medium' conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null) - def container_image = "/snp-sites:2.5.1--hed695b0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "snp-sites:2.5.1--hed695b0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 086f1bb9969..4f40d0675f3 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -4,8 +4,9 @@ process SOMALIER_EXTRACT { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - def container_image = "/somalier:0.2.15--h37c5b7d_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "somalier:0.2.15--h37c5b7d_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index dcc0a37b5cd..cffbd5321ea 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -4,8 +4,9 @@ process SOMALIER_RELATE { label 'process_low' conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null) - def container_image = "/somalier:0.2.15--h37c5b7d_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "somalier:0.2.15--h37c5b7d_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(extract) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index e3da3a8b0ce..c3bafec266c 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,8 +3,9 @@ process SORTMERNA { label "process_high" conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null) - def container_image = "/sortmerna:4.3.4--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sortmerna:4.3.4--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index 26a37ef14f2..b4d4bcac3c2 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -3,8 +3,9 @@ process SOURMASH_SKETCH { label 'process_low' conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) - def container_image = "/sourmash:4.2.4--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sourmash:4.2.4--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 2b043094781..f47469e36b4 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -3,8 +3,9 @@ process SPADES { label 'process_high' conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null) - def container_image = "/spades:3.15.4--h95f258a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "spades:3.15.4--h95f258a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index f1d4d6c097b..c6031651802 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -3,8 +3,9 @@ process SPATYPER { label 'process_low' conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null) - def container_image = "/spatyper:0.3.3--pyhdfd78af_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "spatyper:0.3.3--pyhdfd78af_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index 7c86a0cf5a6..890ffa7ced0 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -3,8 +3,9 @@ process SRATOOLS_FASTERQDUMP { label 'process_medium' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null) - def container_image = "/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index b73ae42af14..7d7a2fe234b 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -3,8 +3,9 @@ process SRATOOLS_PREFETCH { label 'process_low' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) - def container_image = "/sra-tools:2.11.0--pl5321ha49a11a_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "sra-tools:2.11.0--pl5321ha49a11a_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), val(id) diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 154f1579c8a..21d2ab8c9ef 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -3,8 +3,9 @@ process SRST2_SRST2 { label 'process_low' conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null) - def container_image = "/srst2:0.2.0--py27_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "srst2:0.2.0--py27_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index c0c9c38f504..c9e0768bab8 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -5,7 +5,8 @@ process SSUISSERO { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null) def container_image = "ssuissero:1.0.1--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index 5d04aedb85f..13f40a48a7a 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -3,8 +3,9 @@ process STADENIOLIB_SCRAMBLE { label 'process_medium' conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null) - def container_image = "/staden_io_lib:1.14.14--h0d9da7e_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "staden_io_lib:1.14.14--h0d9da7e_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index c5fd2fd028b..754e655ca7a 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -3,8 +3,9 @@ process STAPHOPIASCCMEC { label 'process_low' conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) - def container_image = "/staphopia-sccmec:1.0.0--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "staphopia-sccmec:1.0.0--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 33575afe002..f8274f6800c 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,8 +3,9 @@ process STAR_ALIGN { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index c0b52157e8b..11abdc5d47d 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,8 +3,9 @@ process STAR_GENOMEGENERATE { label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) - def container_image = "/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 5fce33dfec3..1e5286ec78d 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -3,8 +3,9 @@ process STRANGER { label 'process_low' conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null) - def container_image = "/stranger:0.8.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "stranger:0.8.1--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index 245ce5d2ab6..fa8c65f5104 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -3,8 +3,9 @@ process STRELKA_GERMLINE { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - def container_image = "/strelka:2.9.10--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "strelka:2.9.10--h9ee0642_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index db73ab1ff4a..1bede8664e5 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -3,8 +3,9 @@ process STRELKA_SOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) - def container_image = "/strelka:2.9.10--h9ee0642_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "strelka:2.9.10--h9ee0642_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 92077e1a3bd..8d4c07ef76a 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -3,8 +3,9 @@ process STRINGTIE_MERGE { // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - def container_image = "/stringtie:2.2.1--hecb563c_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "stringtie:2.2.1--hecb563c_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index c06a17adea9..22812ee6376 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -3,8 +3,9 @@ process STRINGTIE_STRINGTIE { label 'process_medium' conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) - def container_image = "/stringtie:2.2.1--hecb563c_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "stringtie:2.2.1--hecb563c_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index c402b8f33fb..9cac56cb70c 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -3,8 +3,9 @@ process SUBREAD_FEATURECOUNTS { label 'process_medium' conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) - def container_image = "/subread:2.0.1--hed695b0_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "subread:2.0.1--hed695b0_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index f12dd0315b2..0c275e8a06e 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -2,8 +2,9 @@ process SVDB_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 4d8763dd684..050fe082200 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -3,8 +3,9 @@ process SVDB_QUERY { label 'process_medium' conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null) - def container_image = "/svdb:2.6.1--py39h5371cbf_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "svdb:2.6.1--py39h5371cbf_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index ae776230e0b..e12bd9f45a5 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -3,8 +3,9 @@ process SVTK_STANDARDIZE { label 'process_low' conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null) - def container_image = "/svtk:0.0.20190615--py37h73a75cf_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "svtk:0.0.20190615--py37h73a75cf_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 2e0eeb697f6..0437e5ae086 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -3,8 +3,9 @@ process TABIX_BGZIP { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - def container_image = "/tabix:1.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "tabix:1.11--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 5582261a2eb..377ebdccd22 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -3,8 +3,9 @@ process TABIX_BGZIPTABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - def container_image = "/tabix:1.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "tabix:1.11--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 747d6872e33..bae79766442 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -3,8 +3,9 @@ process TABIX_TABIX { label 'process_single' conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) - def container_image = "/tabix:1.11--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "tabix:1.11--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 706006d3bbe..30932b5470c 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -3,8 +3,9 @@ process TAILFINDR { label 'process_high' conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null) - def container_image = "/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index ae7250f67fe..b005e59acce 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -3,8 +3,9 @@ process TBPROFILER_PROFILE { label 'process_medium' conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null) - def container_image = "/tb-profiler:3.0.8--pypyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "tb-profiler:3.0.8--pypyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 8720e29a339..e0f93785459 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -3,8 +3,9 @@ process TIDDIT_COV { label 'process_low' conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null) - def container_image = "/tiddit:3.0.0--py39h59fae87_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "tiddit:3.0.0--py39h59fae87_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input) diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 7720552e3e8..38ea627df7f 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -3,8 +3,9 @@ process TIDDIT_SV { label 'process_medium' conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null) - def container_image = "/tiddit:3.1.0--py39h59fae87_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "tiddit:3.1.0--py39h59fae87_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index 3d0bcbf92d6..48ecac9b8c1 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -3,8 +3,9 @@ process TRANSDECODER_LONGORF { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" - container { (params.container_registry ?: 'quay.io/comp-bio-aging' + container_image) } + def container_image = "transdecoder:5.5.0--pl5262hdfd78af_4" + container [ params.container_registry ?: 'quay.io/comp-bio-aging' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index 42833f5e269..08ae6c4c629 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -3,8 +3,9 @@ process TRANSDECODER_PREDICT { label 'process_medium' conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null) - def container_image = "/transdecoder:5.5.0--pl5262hdfd78af_4" - container { (params.container_registry ?: 'quay.io/comp-bio-aging' + container_image) } + def container_image = "transdecoder:5.5.0--pl5262hdfd78af_4" + container [ params.container_registry ?: 'quay.io/comp-bio-aging' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 1dc9f353eaf..7c76791d17f 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -3,8 +3,9 @@ process TRIMGALORE { label 'process_high' conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) - def container_image = "/trim-galore:0.6.7--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "trim-galore:0.6.7--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index c48e1165363..0f1dad5ab66 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -3,8 +3,9 @@ process TRIMMOMATIC { label 'process_medium' conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null) - def container_image = "/trimmomatic:0.39--hdfd78af_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "trimmomatic:0.39--hdfd78af_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index 1a92d7de486..f74f4d6df1d 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -4,8 +4,9 @@ process UCSC_BEDCLIP { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null) - def container_image = "/ucsc-bedclip:377--h0b8a92a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ucsc-bedclip:377--h0b8a92a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 0e453a43711..866eef98d3d 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -4,8 +4,9 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) - def container_image = "/ucsc-bedgraphtobigwig:377--h446ed27_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ucsc-bedgraphtobigwig:377--h446ed27_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bedgraph) diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index d7a398a64c2..afa558e97e7 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -4,8 +4,9 @@ process UCSC_BEDTOBIGBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null) - def container_image = "/ucsc-bedtobigbed:377--ha8a8165_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ucsc-bedtobigbed:377--ha8a8165_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index d9fa3f32fd7..dc3ad8983c7 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -4,8 +4,9 @@ process UCSC_BIGWIGAVERAGEOVERBED { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null) - def container_image = "/ucsc-bigwigaverageoverbed:377--h0b8a92a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ucsc-bigwigaverageoverbed:377--h0b8a92a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index 99e795e6014..d606545e92b 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -4,8 +4,9 @@ process UCSC_LIFTOVER { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null) - def container_image = "/ucsc-liftover:377--h0b8a92a_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ucsc-liftover:377--h0b8a92a_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bed) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 7148ae9aade..0156ead4ce2 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -4,8 +4,9 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null) - def container_image = "/ucsc-wigtobigwig:377--h0b8a92a_2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ucsc-wigtobigwig:377--h0b8a92a_2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(wig) diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index 2c5e5e3d999..7078f0ccd32 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -3,8 +3,9 @@ process ULTRA_ALIGN { label 'process_medium' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 4ab4d258713..59b66fefc59 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -3,8 +3,9 @@ process ULTRA_INDEX { label 'process_low' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4" : null) - def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: path fasta diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index cd187d1313c..c2bae6b2714 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -3,8 +3,9 @@ process ULTRA_PIPELINE { label 'process_high' conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null) - def container_image = "/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index c02829893a8..f8501646a5f 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -3,8 +3,9 @@ process UMITOOLS_DEDUP { label "process_medium" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "umi_tools:1.1.2--py38h4a8c8d9_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 552ed09e66d..96d67cded0a 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -3,8 +3,9 @@ process UMITOOLS_EXTRACT { label "process_low" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) - def container_image = "/umi_tools:1.1.2--py38h4a8c8d9_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "umi_tools:1.1.2--py38h4a8c8d9_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index a78dbec983e..c0d80106eb8 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -3,8 +3,9 @@ process UNICYCLER { label 'process_high' conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) - def container_image = "/unicycler:0.4.8--py38h8162308_3" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "unicycler:0.4.8--py38h8162308_3" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 7a2bb197c64..22cc5b7a66e 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -3,8 +3,9 @@ process UNTAR { label 'process_single' conda (params.enable_conda ? "conda-forge::sed=4.7" : null) - def container_image = "/ubuntu:20.04" - container { (params.container_registry ?: '' + container_image) } + def container_image = "ubuntu:20.04" + container [ params.container_registry ?: '' , container_image ].join('/') + input: tuple val(meta), path(archive) diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index 6771513823c..f6a92ebd0d6 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -3,8 +3,9 @@ process UNZIP { label 'process_single' conda (params.enable_conda ? "bioconda::p7zip=15.09" : null) - def container_image = "/p7zip:15.09--h2d50403_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "p7zip:15.09--h2d50403_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 43cd571b9ee..a68cebbed3d 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -3,8 +3,9 @@ process VARDICTJAVA { label 'process_medium' conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) - def container_image = "/vardict-java:1.8.3--hdfd78af_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vardict-java:1.8.3--hdfd78af_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index c0bb54bd536..83f3ab7b4c9 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -4,8 +4,9 @@ process VARIANTBAM { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null) - def container_image = "/variantbam:1.4.4a--h7d7f7ad_5" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "variantbam:1.4.4a--h7d7f7ad_5" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 176948798e6..1406efb6c0c 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,8 +4,9 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null) - def container_image = "/vcf2db:2020.02.24--hdfd78af_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vcf2db:2020.02.24--hdfd78af_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index dddef79f9ac..ff589d0ec51 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -5,8 +5,9 @@ process VCF2MAF { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null) - def container_image = "/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index cfd8a012f0a..60d4b9e3ebe 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -3,8 +3,9 @@ process VCFANNO { label 'process_low' conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) - def container_image = "/vcfanno:0.3.3--h9ee0642_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vcfanno:0.3.3--h9ee0642_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index bb802f2884f..7af1752dc5a 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -3,8 +3,9 @@ process VCFLIB_VCFBREAKMULTI { label 'process_low' conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - def container_image = "/vcflib:1.0.3--hecb563c_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vcflib:1.0.3--hecb563c_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index 5c8a5fc3ce6..263f88fefaa 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -4,8 +4,9 @@ process VCFLIB_VCFUNIQ { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) - def container_image = "/vcflib:1.0.3--hecb563c_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vcflib:1.0.3--hecb563c_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index 82be8643bf3..18c11e296da 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -3,8 +3,9 @@ process VCFTOOLS { label 'process_single' conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null) - def container_image = "/vcftools:0.1.16--he513fc3_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vcftools:0.1.16--he513fc3_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 118064fc94c..8f9931f56f2 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,8 +3,9 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda (params.enable_conda ? "bioconda::verifybamid2=2.0.1" : null) - def container_image = "/verifybamid2:2.0.1--hbb20b25_6" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "verifybamid2:2.0.1--hbb20b25_6" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 1f8fe19cc0f..0110e1eab4d 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -3,8 +3,9 @@ process VSEARCH_SINTAX { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - def container_image = "/vsearch:2.21.1--h95f258a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vsearch:2.21.1--h95f258a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index e7eafbb6b1d..ea25a7f53e4 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -3,8 +3,9 @@ process VSEARCH_USEARCHGLOBAL { label 'process_low' conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null) - def container_image = "/vsearch:2.21.1--h95f258a_0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "vsearch:2.21.1--h95f258a_0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index d022ad10337..d5a0fbc6eeb 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -3,8 +3,9 @@ process WGSIM { label 'process_medium' conda (params.enable_conda ? "bioconda::wgsim=1.0" : null) - def container_image = "/wgsim:1.0--h5bf99c6_4" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "wgsim:1.0--h5bf99c6_4" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index ab94ee060a8..3de742a390c 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -3,8 +3,9 @@ process WHAMG { label 'process_medium' conda (params.enable_conda ? "bioconda::wham=1.8.0" : null) - def container_image = "/wham:1.8.0.1.2017.05.03--h8b12597_1" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "wham:1.8.0.1.2017.05.03--h8b12597_1" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index cf1750056ab..27cb24590ad 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -3,8 +3,9 @@ process YARA_INDEX { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) - def container_image = "/yara:1.0.2--2" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "yara:1.0.2--2" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 4e57137ef7b..07a2371d2ea 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -3,8 +3,9 @@ process YARA_MAPPER { label 'process_medium' conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null) - def container_image = "/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" - container { (params.container_registry ?: 'quay.io/biocontainers' + container_image) } + def container_image = "mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" + container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') + input: tuple val(meta), path(reads) From f94adb3c09183cfd26e75dff82b21d3957af21c1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 16 Oct 2022 16:04:50 -0500 Subject: [PATCH 21/21] style: Remove all double spaces find modules -name 'main.nf' -exec sh -c 'cat -s $0 > $0_new' {} \; find modules -name 'main.nf' -exec rm {} \; fd main.nf_new modules -x rename '_new' '' -v \; --- modules/nf-core/abacas/main.nf | 1 - modules/nf-core/abricate/run/main.nf | 1 - modules/nf-core/abricate/summary/main.nf | 1 - modules/nf-core/adapterremoval/main.nf | 1 - modules/nf-core/adapterremovalfixprefix/main.nf | 1 - modules/nf-core/agrvate/main.nf | 1 - modules/nf-core/allelecounter/main.nf | 1 - modules/nf-core/ampir/main.nf | 1 - modules/nf-core/amplify/predict/main.nf | 1 - modules/nf-core/amps/main.nf | 1 - modules/nf-core/amrfinderplus/run/main.nf | 1 - modules/nf-core/amrfinderplus/update/main.nf | 1 - modules/nf-core/angsd/docounts/main.nf | 1 - modules/nf-core/antismash/antismashlite/main.nf | 1 - .../nf-core/antismash/antismashlitedownloaddatabases/main.nf | 1 - modules/nf-core/aria2/main.nf | 1 - modules/nf-core/ariba/getref/main.nf | 1 - modules/nf-core/ariba/run/main.nf | 1 - modules/nf-core/arriba/main.nf | 1 - modules/nf-core/artic/guppyplex/main.nf | 1 - modules/nf-core/artic/minion/main.nf | 1 - modules/nf-core/ascat/main.nf | 3 --- modules/nf-core/assemblyscan/main.nf | 1 - modules/nf-core/ataqv/ataqv/main.nf | 1 - modules/nf-core/ataqv/mkarv/main.nf | 1 - modules/nf-core/atlas/call/main.nf | 2 -- modules/nf-core/atlas/pmd/main.nf | 1 - modules/nf-core/atlas/recal/main.nf | 1 - modules/nf-core/atlas/splitmerge/main.nf | 1 - modules/nf-core/bakta/main.nf | 1 - modules/nf-core/bamaligncleaner/main.nf | 1 - modules/nf-core/bamcmp/main.nf | 1 - modules/nf-core/bamtools/convert/main.nf | 1 - modules/nf-core/bamtools/split/main.nf | 1 - modules/nf-core/bamtools/stats/main.nf | 1 - modules/nf-core/bamutil/trimbam/main.nf | 1 - modules/nf-core/bandage/image/main.nf | 1 - modules/nf-core/bbmap/align/main.nf | 1 - modules/nf-core/bbmap/bbduk/main.nf | 1 - modules/nf-core/bbmap/bbsplit/main.nf | 1 - modules/nf-core/bbmap/clumpify/main.nf | 1 - modules/nf-core/bbmap/index/main.nf | 1 - modules/nf-core/bbmap/pileup/main.nf | 1 - modules/nf-core/bcftools/annotate/main.nf | 1 - modules/nf-core/bcftools/concat/main.nf | 1 - modules/nf-core/bcftools/consensus/main.nf | 1 - modules/nf-core/bcftools/convert/main.nf | 1 - modules/nf-core/bcftools/filter/main.nf | 1 - modules/nf-core/bcftools/index/main.nf | 1 - modules/nf-core/bcftools/isec/main.nf | 1 - modules/nf-core/bcftools/merge/main.nf | 1 - modules/nf-core/bcftools/mpileup/main.nf | 1 - modules/nf-core/bcftools/norm/main.nf | 1 - modules/nf-core/bcftools/query/main.nf | 1 - modules/nf-core/bcftools/reheader/main.nf | 1 - modules/nf-core/bcftools/roh/main.nf | 1 - modules/nf-core/bcftools/sort/main.nf | 1 - modules/nf-core/bcftools/stats/main.nf | 1 - modules/nf-core/bcftools/view/main.nf | 1 - modules/nf-core/bedtools/bamtobed/main.nf | 1 - modules/nf-core/bedtools/complement/main.nf | 1 - modules/nf-core/bedtools/genomecov/main.nf | 1 - modules/nf-core/bedtools/getfasta/main.nf | 1 - modules/nf-core/bedtools/intersect/main.nf | 1 - modules/nf-core/bedtools/makewindows/main.nf | 1 - modules/nf-core/bedtools/maskfasta/main.nf | 1 - modules/nf-core/bedtools/merge/main.nf | 1 - modules/nf-core/bedtools/slop/main.nf | 1 - modules/nf-core/bedtools/sort/main.nf | 1 - modules/nf-core/bedtools/split/main.nf | 1 - modules/nf-core/bedtools/subtract/main.nf | 1 - modules/nf-core/biobambam/bammarkduplicates2/main.nf | 1 - modules/nf-core/biobambam/bammerge/main.nf | 1 - modules/nf-core/biobambam/bamsormadup/main.nf | 1 - modules/nf-core/biscuit/align/main.nf | 2 -- modules/nf-core/biscuit/biscuitblaster/main.nf | 1 - modules/nf-core/biscuit/bsconv/main.nf | 1 - modules/nf-core/biscuit/epiread/main.nf | 1 - modules/nf-core/biscuit/index/main.nf | 1 - modules/nf-core/biscuit/mergecg/main.nf | 1 - modules/nf-core/biscuit/pileup/main.nf | 1 - modules/nf-core/biscuit/qc/main.nf | 1 - modules/nf-core/biscuit/vcf2bed/main.nf | 1 - modules/nf-core/bismark/align/main.nf | 1 - modules/nf-core/bismark/deduplicate/main.nf | 1 - modules/nf-core/bismark/genomepreparation/main.nf | 1 - modules/nf-core/bismark/methylationextractor/main.nf | 1 - modules/nf-core/bismark/report/main.nf | 1 - modules/nf-core/bismark/summary/main.nf | 1 - modules/nf-core/blast/blastn/main.nf | 1 - modules/nf-core/blast/makeblastdb/main.nf | 1 - modules/nf-core/blast/tblastn/main.nf | 1 - modules/nf-core/bowtie2/align/main.nf | 1 - modules/nf-core/bowtie2/build/main.nf | 1 - modules/nf-core/bracken/bracken/main.nf | 1 - modules/nf-core/bracken/combinebrackenoutputs/main.nf | 1 - modules/nf-core/busco/main.nf | 1 - modules/nf-core/bwa/aln/main.nf | 1 - modules/nf-core/bwa/index/main.nf | 1 - modules/nf-core/bwa/mem/main.nf | 1 - modules/nf-core/bwa/sampe/main.nf | 1 - modules/nf-core/bwa/samse/main.nf | 1 - modules/nf-core/bwamem2/index/main.nf | 1 - modules/nf-core/bwamem2/mem/main.nf | 1 - modules/nf-core/bwameth/align/main.nf | 1 - modules/nf-core/bwameth/index/main.nf | 1 - modules/nf-core/cat/cat/main.nf | 1 - modules/nf-core/cat/fastq/main.nf | 1 - modules/nf-core/centrifuge/centrifuge/main.nf | 1 - modules/nf-core/centrifuge/kreport/main.nf | 1 - modules/nf-core/checkm/lineagewf/main.nf | 1 - modules/nf-core/checkm/qa/main.nf | 1 - modules/nf-core/chromap/chromap/main.nf | 1 - modules/nf-core/chromap/index/main.nf | 1 - modules/nf-core/clonalframeml/main.nf | 1 - modules/nf-core/cmseq/polymut/main.nf | 1 - modules/nf-core/cnvkit/antitarget/main.nf | 1 - modules/nf-core/cnvkit/batch/main.nf | 1 - modules/nf-core/cnvkit/reference/main.nf | 1 - modules/nf-core/cnvpytor/callcnvs/main.nf | 1 - modules/nf-core/cnvpytor/histogram/main.nf | 2 -- modules/nf-core/cnvpytor/importreaddepth/main.nf | 1 - modules/nf-core/cnvpytor/partition/main.nf | 1 - modules/nf-core/cnvpytor/view/main.nf | 1 - modules/nf-core/controlfreec/assesssignificance/main.nf | 1 - modules/nf-core/controlfreec/freec/main.nf | 1 - modules/nf-core/controlfreec/freec2bed/main.nf | 1 - modules/nf-core/controlfreec/freec2circos/main.nf | 1 - modules/nf-core/controlfreec/makegraph/main.nf | 1 - modules/nf-core/cooler/cload/main.nf | 1 - modules/nf-core/cooler/digest/main.nf | 1 - modules/nf-core/cooler/dump/main.nf | 1 - modules/nf-core/cooler/merge/main.nf | 1 - modules/nf-core/cooler/zoomify/main.nf | 1 - modules/nf-core/crumble/main.nf | 1 - modules/nf-core/csvtk/concat/main.nf | 1 - modules/nf-core/csvtk/split/main.nf | 1 - modules/nf-core/custom/dumpsoftwareversions/main.nf | 1 - modules/nf-core/custom/getchromsizes/main.nf | 1 - modules/nf-core/custom/sratoolsncbisettings/main.nf | 1 - modules/nf-core/cutadapt/main.nf | 1 - modules/nf-core/damageprofiler/main.nf | 1 - modules/nf-core/dastool/dastool/main.nf | 1 - modules/nf-core/dastool/fastatocontig2bin/main.nf | 1 - modules/nf-core/dastool/scaffolds2bin/main.nf | 1 - modules/nf-core/dedup/main.nf | 1 - modules/nf-core/deeparg/downloaddata/main.nf | 1 - modules/nf-core/deepbgc/download/main.nf | 1 - modules/nf-core/deepbgc/pipeline/main.nf | 1 - modules/nf-core/deeptools/bamcoverage/main.nf | 1 - modules/nf-core/deeptools/computematrix/main.nf | 1 - modules/nf-core/deeptools/plotfingerprint/main.nf | 1 - modules/nf-core/deeptools/plotheatmap/main.nf | 1 - modules/nf-core/deeptools/plotprofile/main.nf | 1 - modules/nf-core/deepvariant/main.nf | 1 - modules/nf-core/delly/call/main.nf | 1 - modules/nf-core/diamond/blastp/main.nf | 1 - modules/nf-core/diamond/blastx/main.nf | 1 - modules/nf-core/diamond/makedb/main.nf | 1 - modules/nf-core/dragmap/align/main.nf | 1 - modules/nf-core/dragmap/hashtable/main.nf | 1 - modules/nf-core/dragonflye/main.nf | 1 - modules/nf-core/dshbio/exportsegments/main.nf | 1 - modules/nf-core/dshbio/filterbed/main.nf | 1 - modules/nf-core/dshbio/filtergff3/main.nf | 1 - modules/nf-core/dshbio/splitbed/main.nf | 1 - modules/nf-core/dshbio/splitgff3/main.nf | 1 - modules/nf-core/ectyper/main.nf | 1 - modules/nf-core/elprep/filter/main.nf | 2 -- modules/nf-core/elprep/merge/main.nf | 1 - modules/nf-core/elprep/split/main.nf | 1 - modules/nf-core/emboss/seqret/main.nf | 1 - modules/nf-core/emmtyper/main.nf | 1 - modules/nf-core/endorspy/main.nf | 1 - modules/nf-core/ensemblvep/main.nf | 2 -- modules/nf-core/entrezdirect/esearch/main.nf | 1 - modules/nf-core/entrezdirect/esummary/main.nf | 1 - modules/nf-core/entrezdirect/xtract/main.nf | 1 - modules/nf-core/epang/main.nf | 1 - modules/nf-core/expansionhunter/main.nf | 1 - modules/nf-core/falco/main.nf | 1 - modules/nf-core/faqcs/main.nf | 2 -- modules/nf-core/fargene/main.nf | 1 - modules/nf-core/fastani/main.nf | 1 - modules/nf-core/fastawindows/main.nf | 1 - modules/nf-core/fastp/main.nf | 1 - modules/nf-core/fastqc/main.nf | 1 - modules/nf-core/fastqscan/main.nf | 1 - modules/nf-core/fasttree/main.nf | 1 - modules/nf-core/ffq/main.nf | 1 - modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 1 - modules/nf-core/fgbio/fastqtobam/main.nf | 1 - modules/nf-core/fgbio/groupreadsbyumi/main.nf | 1 - modules/nf-core/fgbio/sortbam/main.nf | 1 - modules/nf-core/fgbio/zipperbams/main.nf | 2 -- modules/nf-core/filtlong/main.nf | 1 - modules/nf-core/flash/main.nf | 1 - modules/nf-core/flye/main.nf | 1 - modules/nf-core/fq/lint/main.nf | 1 - modules/nf-core/freebayes/main.nf | 1 - modules/nf-core/gamma/gamma/main.nf | 1 - modules/nf-core/gappa/examineassign/main.nf | 1 - modules/nf-core/gappa/examinegraft/main.nf | 1 - modules/nf-core/gappa/examineheattree/main.nf | 1 - modules/nf-core/gatk/indelrealigner/main.nf | 1 - modules/nf-core/gatk/realignertargetcreator/main.nf | 1 - modules/nf-core/gatk/unifiedgenotyper/main.nf | 1 - modules/nf-core/gatk4/applybqsr/main.nf | 1 - modules/nf-core/gatk4/applyvqsr/main.nf | 1 - modules/nf-core/gatk4/baserecalibrator/main.nf | 1 - modules/nf-core/gatk4/bedtointervallist/main.nf | 1 - modules/nf-core/gatk4/calculatecontamination/main.nf | 1 - modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 1 - modules/nf-core/gatk4/collectreadcounts/main.nf | 1 - modules/nf-core/gatk4/collectsvevidence/main.nf | 1 - modules/nf-core/gatk4/combinegvcfs/main.nf | 1 - modules/nf-core/gatk4/composestrtablefile/main.nf | 1 - modules/nf-core/gatk4/createsequencedictionary/main.nf | 1 - modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 1 - modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 1 - modules/nf-core/gatk4/fastqtosam/main.nf | 1 - modules/nf-core/gatk4/filtermutectcalls/main.nf | 1 - modules/nf-core/gatk4/filtervarianttranches/main.nf | 2 -- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 1 - modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 2 -- modules/nf-core/gatk4/genomicsdbimport/main.nf | 1 - modules/nf-core/gatk4/genotypegvcfs/main.nf | 1 - modules/nf-core/gatk4/getpileupsummaries/main.nf | 1 - modules/nf-core/gatk4/haplotypecaller/main.nf | 1 - modules/nf-core/gatk4/indexfeaturefile/main.nf | 1 - modules/nf-core/gatk4/intervallisttobed/main.nf | 1 - modules/nf-core/gatk4/intervallisttools/main.nf | 1 - modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 1 - modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 1 - modules/nf-core/gatk4/markduplicates/main.nf | 2 -- modules/nf-core/gatk4/markduplicatesspark/main.nf | 1 - modules/nf-core/gatk4/mergebamalignment/main.nf | 1 - modules/nf-core/gatk4/mergemutectstats/main.nf | 1 - modules/nf-core/gatk4/mergevcfs/main.nf | 1 - modules/nf-core/gatk4/mutect2/main.nf | 1 - modules/nf-core/gatk4/printsvevidence/main.nf | 1 - modules/nf-core/gatk4/reblockgvcf/main.nf | 1 - modules/nf-core/gatk4/revertsam/main.nf | 1 - modules/nf-core/gatk4/samtofastq/main.nf | 1 - modules/nf-core/gatk4/selectvariants/main.nf | 1 - modules/nf-core/gatk4/splitintervals/main.nf | 1 - modules/nf-core/gatk4/splitncigarreads/main.nf | 1 - modules/nf-core/gatk4/variantfiltration/main.nf | 1 - modules/nf-core/gatk4/variantrecalibrator/main.nf | 1 - modules/nf-core/gecco/run/main.nf | 2 -- modules/nf-core/genmap/index/main.nf | 1 - modules/nf-core/genmap/mappability/main.nf | 1 - modules/nf-core/genmod/annotate/main.nf | 1 - modules/nf-core/genmod/compound/main.nf | 1 - modules/nf-core/genmod/models/main.nf | 1 - modules/nf-core/genmod/score/main.nf | 1 - modules/nf-core/genomescope2/main.nf | 1 - modules/nf-core/genotyphi/parse/main.nf | 1 - modules/nf-core/genrich/main.nf | 1 - modules/nf-core/gfaffix/main.nf | 1 - modules/nf-core/gffread/main.nf | 1 - modules/nf-core/glimpse/chunk/main.nf | 1 - modules/nf-core/glnexus/main.nf | 1 - modules/nf-core/goat/taxonsearch/main.nf | 1 - modules/nf-core/graphmap2/align/main.nf | 1 - modules/nf-core/graphmap2/index/main.nf | 1 - modules/nf-core/gstama/collapse/main.nf | 1 - modules/nf-core/gstama/merge/main.nf | 1 - modules/nf-core/gstama/polyacleanup/main.nf | 1 - modules/nf-core/gtdbtk/classifywf/main.nf | 1 - modules/nf-core/gubbins/main.nf | 1 - modules/nf-core/gunc/downloaddb/main.nf | 1 - modules/nf-core/gunc/run/main.nf | 1 - modules/nf-core/gunzip/main.nf | 1 - modules/nf-core/gvcftools/extractvariants/main.nf | 1 - modules/nf-core/hamronization/abricate/main.nf | 2 -- modules/nf-core/hamronization/amrfinderplus/main.nf | 1 - modules/nf-core/hamronization/deeparg/main.nf | 2 -- modules/nf-core/hamronization/fargene/main.nf | 1 - modules/nf-core/hamronization/rgi/main.nf | 1 - modules/nf-core/hamronization/summarize/main.nf | 1 - modules/nf-core/haplocheck/main.nf | 1 - modules/nf-core/haplogrep2/classify/main.nf | 1 - modules/nf-core/happy/happy/main.nf | 1 - modules/nf-core/happy/prepy/main.nf | 1 - modules/nf-core/hicap/main.nf | 1 - modules/nf-core/hifiasm/main.nf | 1 - modules/nf-core/hisat2/align/main.nf | 1 - modules/nf-core/hisat2/build/main.nf | 1 - modules/nf-core/hisat2/extractsplicesites/main.nf | 1 - modules/nf-core/hmmcopy/gccounter/main.nf | 1 - 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modules/nf-core/yara/index/main.nf | 1 - modules/nf-core/yara/mapper/main.nf | 1 - 615 files changed, 636 deletions(-) mode change 100755 => 100644 modules/nf-core/ucsc/bedclip/main.nf diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index ab957c095f4..f8663cd4f6d 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -6,7 +6,6 @@ process ABACAS { def container_image = "abacas:1.3.1--pl526_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(scaffold) path fasta diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf index a3780f3fbf5..bb80d54857b 100644 --- a/modules/nf-core/abricate/run/main.nf +++ b/modules/nf-core/abricate/run/main.nf @@ -6,7 +6,6 @@ process ABRICATE_RUN { def container_image = "abricate:1.0.1--ha8f3691_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf index ab1f7dfa965..d3471feac25 100644 --- a/modules/nf-core/abricate/summary/main.nf +++ b/modules/nf-core/abricate/summary/main.nf @@ -6,7 +6,6 @@ process ABRICATE_SUMMARY { def container_image = "abricate:1.0.1--ha8f3691_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reports) diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index e792330df0d..62d8c0356c4 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -6,7 +6,6 @@ process ADAPTERREMOVAL { def container_image = "adapterremoval:2.3.2--hb7ba0dd_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path(adapterlist) diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf index 9cf5ebb3167..c1ee8fac866 100644 --- a/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/modules/nf-core/adapterremovalfixprefix/main.nf @@ -7,7 +7,6 @@ process ADAPTERREMOVALFIXPREFIX { def container_image = "adapterremovalfixprefix:0.0.5--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf index 3ff000f21de..1491800ceba 100644 --- a/modules/nf-core/agrvate/main.nf +++ b/modules/nf-core/agrvate/main.nf @@ -6,7 +6,6 @@ process AGRVATE { def container_image = "agrvate:1.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf index 6e4803ece3e..0cc9b28f351 100644 --- a/modules/nf-core/allelecounter/main.nf +++ b/modules/nf-core/allelecounter/main.nf @@ -6,7 +6,6 @@ process ALLELECOUNTER { def container_image = "cancerit-allelecount:4.3.0--h41abebc_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index) path loci diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf index ac80298f05a..4b1f146a99c 100644 --- a/modules/nf-core/ampir/main.nf +++ b/modules/nf-core/ampir/main.nf @@ -6,7 +6,6 @@ process AMPIR { def container_image = "r-ampir:1.1.0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(faa) val model diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf index 940a78c1ef2..a87afb0fc60 100644 --- a/modules/nf-core/amplify/predict/main.nf +++ b/modules/nf-core/amplify/predict/main.nf @@ -7,7 +7,6 @@ process AMPLIFY_PREDICT { def container_image = "amplify:1.0.3--py36hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(faa) path(model_dir) diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf index 8f437f1f45f..8e6005e18c3 100644 --- a/modules/nf-core/amps/main.nf +++ b/modules/nf-core/amps/main.nf @@ -5,7 +5,6 @@ process AMPS { def container_image = "hops:0.35--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path maltextract_results path taxon_list diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index ae4f77df085..3fa1679caa1 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -6,7 +6,6 @@ process AMRFINDERPLUS_RUN { def container_image = "ncbi-amrfinderplus:3.10.30--h6e70893_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path db diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index 5f2ea0c8d58..4867670dba9 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -6,7 +6,6 @@ process AMRFINDERPLUS_UPDATE { def container_image = "ncbi-amrfinderplus:3.10.30--h6e70893_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - output: path "amrfinderdb.tar.gz", emit: db path "versions.yml" , emit: versions diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf index bd6f6dffb34..459401fea38 100644 --- a/modules/nf-core/angsd/docounts/main.nf +++ b/modules/nf-core/angsd/docounts/main.nf @@ -6,7 +6,6 @@ process ANGSD_DOCOUNTS { def container_image = "angsd:0.939--h468462d_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(minqfile) diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 8132ee9ca16..74f054187b4 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -6,7 +6,6 @@ process ANTISMASH_ANTISMASHLITE { def container_image = "antismash-lite:6.0.1--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - containerOptions { workflow.containerEngine == 'singularity' ? "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" : diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 00249d481b4..d492b44e456 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -5,7 +5,6 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { def container_image = "antismash-lite:6.0.1--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them. diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf index 0bd96d4baf7..c857489daa8 100644 --- a/modules/nf-core/aria2/main.nf +++ b/modules/nf-core/aria2/main.nf @@ -7,7 +7,6 @@ process ARIA2 { def container_image = "aria2:1.36.0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: val source_url diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf index b4adfec2e32..301e95e5e6b 100644 --- a/modules/nf-core/ariba/getref/main.nf +++ b/modules/nf-core/ariba/getref/main.nf @@ -6,7 +6,6 @@ process ARIBA_GETREF { def container_image = "ariba:2.14.6--py39h67e14b5_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: val(db_name) diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf index 3686e776896..c3f681559c1 100644 --- a/modules/nf-core/ariba/run/main.nf +++ b/modules/nf-core/ariba/run/main.nf @@ -6,7 +6,6 @@ process ARIBA_RUN { def container_image = "ariba:2.14.6--py39h67e14b5_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) each path(db) diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index 1edcab1e1b9..8b587c678d6 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -6,7 +6,6 @@ process ARRIBA { def container_image = "arriba:2.3.0--haa8aa89_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 2f18199e6aa..7974a6c60cf 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -6,7 +6,6 @@ process ARTIC_GUPPYPLEX { def container_image = "artic:1.2.2--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index 5a6f3e09ad6..f422152d614 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -6,7 +6,6 @@ process ARTIC_MINION { def container_image = "artic:1.2.2--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq) path fast5_dir diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index eae9f5ee0fb..54e3441d522 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -6,7 +6,6 @@ process ASCAT { def container_image = "mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) path(allele_files) @@ -84,7 +83,6 @@ process ASCAT { $skip_allele_counting_normal_arg ) - #Load the data ascat.bc = ascat.loadData( Tumor_LogR_file = paste0("$prefix", ".tumour_tumourLogR.txt"), @@ -195,5 +193,4 @@ process ASCAT { """ - } diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf index 4d909e66785..4c53ae9c71b 100644 --- a/modules/nf-core/assemblyscan/main.nf +++ b/modules/nf-core/assemblyscan/main.nf @@ -6,7 +6,6 @@ process ASSEMBLYSCAN { def container_image = "assembly-scan:0.4.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(assembly) diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf index b39bb5c8b8f..2ae6146392e 100644 --- a/modules/nf-core/ataqv/ataqv/main.nf +++ b/modules/nf-core/ataqv/ataqv/main.nf @@ -6,7 +6,6 @@ process ATAQV_ATAQV { def container_image = "ataqv:1.3.0--py39hccc85d7_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(peak_file) val organism diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 5a98b849ff0..a9b31a45b9e 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -5,7 +5,6 @@ process ATAQV_MKARV { def container_image = "ataqv:1.3.0--py39hccc85d7_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path json diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf index 64250b28f01..cc23bd36075 100644 --- a/modules/nf-core/atlas/call/main.nf +++ b/modules/nf-core/atlas/call/main.nf @@ -6,7 +6,6 @@ process ATLAS_CALL { def container_image = "atlas:0.9.9--h082e891_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(pmd), path(recal) path fasta @@ -42,7 +41,6 @@ process ATLAS_CALL { method=${method} \\ $args - cat <<-END_VERSIONS > versions.yml "${task.process}": atlas: \$((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //') diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf index be60c87e9d5..6e77bb9d3b1 100644 --- a/modules/nf-core/atlas/pmd/main.nf +++ b/modules/nf-core/atlas/pmd/main.nf @@ -6,7 +6,6 @@ process ATLAS_PMD { def container_image = "atlas:0.9.9--h082e891_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(pool_rg_txt) path(fasta) diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf index ded7aaa498d..ad5a4600f30 100644 --- a/modules/nf-core/atlas/recal/main.nf +++ b/modules/nf-core/atlas/recal/main.nf @@ -6,7 +6,6 @@ process ATLAS_RECAL { def container_image = "atlas:0.9.9--h082e891_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups) path(alleles) diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf index a3fcb66c732..a59e2a552fb 100644 --- a/modules/nf-core/atlas/splitmerge/main.nf +++ b/modules/nf-core/atlas/splitmerge/main.nf @@ -6,7 +6,6 @@ process ATLAS_SPLITMERGE { def container_image = "atlas:0.9.9--h082e891_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist) diff --git a/modules/nf-core/bakta/main.nf b/modules/nf-core/bakta/main.nf index 6dab17a956b..e97db7e401f 100644 --- a/modules/nf-core/bakta/main.nf +++ b/modules/nf-core/bakta/main.nf @@ -6,7 +6,6 @@ process BAKTA { def container_image = "bakta:1.5.0--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path db diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf index 34e42443eda..722a2d370e3 100644 --- a/modules/nf-core/bamaligncleaner/main.nf +++ b/modules/nf-core/bamaligncleaner/main.nf @@ -6,7 +6,6 @@ process BAMALIGNCLEANER { def container_image = "bamaligncleaner:0.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf index 58e5f96d1a8..4f0b83db65a 100644 --- a/modules/nf-core/bamcmp/main.nf +++ b/modules/nf-core/bamcmp/main.nf @@ -6,7 +6,6 @@ process BAMCMP { def container_image = "bamcmp:2.2--h05f6578_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(sample), path(contaminant) diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index efa414adec4..6886b5cd61c 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -6,7 +6,6 @@ process BAMTOOLS_CONVERT { def container_image = "bamtools:2.5.1--h9a82719_9" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf index 559f72c33c7..23726cc25d6 100644 --- a/modules/nf-core/bamtools/split/main.nf +++ b/modules/nf-core/bamtools/split/main.nf @@ -6,7 +6,6 @@ process BAMTOOLS_SPLIT { def container_image = "bamtools:2.5.2--hd03093a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf index 75a0c6820ca..39a7b4c2115 100644 --- a/modules/nf-core/bamtools/stats/main.nf +++ b/modules/nf-core/bamtools/stats/main.nf @@ -6,7 +6,6 @@ process BAMTOOLS_STATS { def container_image = "bamtools:2.5.1--h9a82719_9" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bamutil/trimbam/main.nf b/modules/nf-core/bamutil/trimbam/main.nf index 89fe23b294e..20e39ff0555 100644 --- a/modules/nf-core/bamutil/trimbam/main.nf +++ b/modules/nf-core/bamutil/trimbam/main.nf @@ -6,7 +6,6 @@ process BAMUTIL_TRIMBAM { def container_image = "bamutil:1.0.15--h2e03b76_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), val(trim_left), val(trim_right) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index 5c04969a6cd..7f362e32a68 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -6,7 +6,6 @@ process BANDAGE_IMAGE { def container_image = "bandage:0.8.1--hc9558a2_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 05f109596a3..998a3fe8831 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -6,7 +6,6 @@ process BBMAP_ALIGN { def container_image = "mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq) path ref diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 6080471700c..29b40cc5597 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -6,7 +6,6 @@ process BBMAP_BBDUK { def container_image = "bbmap:38.90--he522d1c_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path contaminants diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 6afe361d2c4..9e5d2d27490 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -5,7 +5,6 @@ process BBMAP_BBSPLIT { def container_image = "bbmap:38.93--he522d1c_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index ef7b4deba43..7e395a073f6 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -7,7 +7,6 @@ process BBMAP_CLUMPIFY { def container_image = "bbmap:38.98--h5c4e2a8_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index e2e5ccd6c66..b0d81219846 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -6,7 +6,6 @@ process BBMAP_INDEX { def container_image = "bbmap:38.92--he522d1c_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 4ff7f61f5fc..c380515feb7 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -6,7 +6,6 @@ process BBMAP_PILEUP { def container_image = "mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 8a7bb4985d7..f8101eef539 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_ANNOTATE { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 247424bf243..93b6dae0f62 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_CONCAT { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index e70a473a197..54cebfdcc9a 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_CONSENSUS { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf index 831805d1c88..eb49028174d 100644 --- a/modules/nf-core/bcftools/convert/main.nf +++ b/modules/nf-core/bcftools/convert/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_CONVERT { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index) path bed diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 3940b137c3a..425e874137e 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_FILTER { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf index 968617d6a0a..4274f3eeca9 100644 --- a/modules/nf-core/bcftools/index/main.nf +++ b/modules/nf-core/bcftools/index/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_INDEX { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf index 76969f3393a..56e3d6dd01b 100644 --- a/modules/nf-core/bcftools/isec/main.nf +++ b/modules/nf-core/bcftools/isec/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_ISEC { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 326746ff691..562c5f2651b 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_MERGE { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcfs), path(tbis) path bed diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index da7e9c6ab52..9223c4e59e1 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_MPILEUP { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 7cf5f8c76b5..73ab6f09528 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_NORM { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) path(fasta) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 0935ef2ca7f..7f839a4f1e3 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_QUERY { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) path regions diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index fbf02b8e378..3d134ac792d 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_REHEADER { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) path fai diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index 27a57b42700..fe689ded454 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_ROH { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) tuple path(af_file), path(af_file_tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index f446531eab4..cbaa679a9c8 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_SORT { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index ef6430dbdca..6fa28b4a7d0 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_STATS { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) path regions diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 1ada6d985a1..3783e4197bd 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -6,7 +6,6 @@ process BCFTOOLS_VIEW { def container_image = "bcftools:1.15.1--h0ea216a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(index) path(regions) diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf index b7ef343cf75..3658fcf627c 100644 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ b/modules/nf-core/bedtools/bamtobed/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_BAMTOBED { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf index 4b8011eb095..113f5dde05a 100644 --- a/modules/nf-core/bedtools/complement/main.nf +++ b/modules/nf-core/bedtools/complement/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_COMPLEMENT { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path sizes diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index f49bcf61d88..1373429d01a 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_GENOMECOV { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals), val(scale) path sizes diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index cd054ea20a4..72bba403c53 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_GETFASTA { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path bed path fasta diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index 56a36f78e4d..186a2b93f1a 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_INTERSECT { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals1), path(intervals2) val extension diff --git a/modules/nf-core/bedtools/makewindows/main.nf b/modules/nf-core/bedtools/makewindows/main.nf index 8afd2b5bef8..4a4bdf5eec1 100644 --- a/modules/nf-core/bedtools/makewindows/main.nf +++ b/modules/nf-core/bedtools/makewindows/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_MAKEWINDOWS { def container_image = "bedtools:2.30.0--h7d7f7ad_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(regions) val(use_bed) diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index a2fb3867ca9..b0e58f7366d 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_MASKFASTA { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path fasta diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 272f6706d3b..ccc72e42c98 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_MERGE { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index 38225e46e47..67a96ac825a 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_SLOP { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path sizes diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 091cc2892c0..fa892a13821 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_SORT { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals) val extension diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index 9a88212efa3..0f572d3acd2 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_SPLIT { def container_image = "bedtools:2.30.0--h468198e_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) val(number_of_files) diff --git a/modules/nf-core/bedtools/subtract/main.nf b/modules/nf-core/bedtools/subtract/main.nf index 94a35d2dc83..03de19b36e6 100644 --- a/modules/nf-core/bedtools/subtract/main.nf +++ b/modules/nf-core/bedtools/subtract/main.nf @@ -6,7 +6,6 @@ process BEDTOOLS_SUBTRACT { def container_image = "bedtools:2.30.0--hc088bd4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/modules/nf-core/biobambam/bammarkduplicates2/main.nf index 6e841a2e148..2a8f533ce6c 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -6,7 +6,6 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 { def container_image = "biobambam:2.0.183--h9f5acd7_1" container (params.container_registry ?: 'quay.io/biocontainers' , container_image) - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bammerge/main.nf b/modules/nf-core/biobambam/bammerge/main.nf index ed4303bf071..08c77b1ef4a 100644 --- a/modules/nf-core/biobambam/bammerge/main.nf +++ b/modules/nf-core/biobambam/bammerge/main.nf @@ -6,7 +6,6 @@ process BIOBAMBAM_BAMMERGE { def container_image = "biobambam:2.0.183--h9f5acd7_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/biobambam/bamsormadup/main.nf b/modules/nf-core/biobambam/bamsormadup/main.nf index 9982e67f600..90f8258d811 100644 --- a/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/modules/nf-core/biobambam/bamsormadup/main.nf @@ -6,7 +6,6 @@ process BIOBAMBAM_BAMSORMADUP { def container_image = "biobambam:2.0.183--h9f5acd7_1" container (params.container_registry ?: 'quay.io/biocontainers' , container_image) - input: tuple val(meta), path(bams, stageAs: "?/*") path(fasta) diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf index 36d8325c992..3880925f76e 100644 --- a/modules/nf-core/biscuit/align/main.nf +++ b/modules/nf-core/biscuit/align/main.nf @@ -6,7 +6,6 @@ process BISCUIT_ALIGN { def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index @@ -34,7 +33,6 @@ process BISCUIT_ALIGN { $reads \\ | samtools sort $args2 --threads $samtools_cpus -o ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml "${task.process}": biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' ) diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf index 47ea80305bb..f8028e8dbdf 100644 --- a/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -6,7 +6,6 @@ process BISCUIT_BLASTER { def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf index 08a7b6e1bf4..5e1ac2fbba1 100644 --- a/modules/nf-core/biscuit/bsconv/main.nf +++ b/modules/nf-core/biscuit/bsconv/main.nf @@ -6,7 +6,6 @@ process BISCUIT_BSCONV { def container_image = "biscuit:1.0.2.20220113--h81a5ba2_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path(index) diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf index 748a08cae6d..a381e3a9ed6 100644 --- a/modules/nf-core/biscuit/epiread/main.nf +++ b/modules/nf-core/biscuit/epiread/main.nf @@ -6,7 +6,6 @@ process BISCUIT_EPIREAD { def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(snp_bed) path(index) diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf index 63d50a23802..8d2785b3f82 100644 --- a/modules/nf-core/biscuit/index/main.nf +++ b/modules/nf-core/biscuit/index/main.nf @@ -6,7 +6,6 @@ process BISCUIT_INDEX { def container_image = "biscuit:1.0.2.20220113--h81a5ba2_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta, stageAs: "BiscuitIndex/*" diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf index d73d86b1fa9..0dd33352c5a 100644 --- a/modules/nf-core/biscuit/mergecg/main.nf +++ b/modules/nf-core/biscuit/mergecg/main.nf @@ -6,7 +6,6 @@ process BISCUIT_MERGECG { def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path index diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf index 2d5ac26234a..dab60272be4 100644 --- a/modules/nf-core/biscuit/pileup/main.nf +++ b/modules/nf-core/biscuit/pileup/main.nf @@ -6,7 +6,6 @@ process BISCUIT_PILEUP { def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai) path index diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf index 882c0a802f4..da20d7f37fa 100644 --- a/modules/nf-core/biscuit/qc/main.nf +++ b/modules/nf-core/biscuit/qc/main.nf @@ -6,7 +6,6 @@ process BISCUIT_QC { def container_image = "biscuit:1.0.2.20220113--h81a5ba2_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path(index) diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf index c4148ae93f1..c5bc5a20ea4 100644 --- a/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/modules/nf-core/biscuit/vcf2bed/main.nf @@ -6,7 +6,6 @@ process BISCUIT_VCF2BED { def container_image = "mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index b6698b9e1fe..947b5a6d65f 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -6,7 +6,6 @@ process BISMARK_ALIGN { def container_image = "bismark:0.23.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index e86dc33363e..fa6d0a1358b 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -6,7 +6,6 @@ process BISMARK_DEDUPLICATE { def container_image = "bismark:0.23.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index de6694ce7ee..84c9e2776a6 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -6,7 +6,6 @@ process BISMARK_GENOMEPREPARATION { def container_image = "bismark:0.23.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta, stageAs: "BismarkIndex/*" diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 9ba0a90d262..dbc17e1c97a 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -6,7 +6,6 @@ process BISMARK_METHYLATIONEXTRACTOR { def container_image = "bismark:0.23.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path index diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 743ef6519c2..4a05ce0fd2a 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -6,7 +6,6 @@ process BISMARK_REPORT { def container_image = "bismark:0.23.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 217f0aea9c1..966557960fa 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -5,7 +5,6 @@ process BISMARK_SUMMARY { def container_image = "bismark:0.23.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path(bam) path(align_report) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index ace1c541a5b..ad31e298007 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -6,7 +6,6 @@ process BLAST_BLASTN { def container_image = "blast:2.12.0--pl5262h3289130_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path db diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 1920d31d168..1c741dfea15 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -6,7 +6,6 @@ process BLAST_MAKEBLASTDB { def container_image = "blast:2.12.0--pl5262h3289130_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/blast/tblastn/main.nf b/modules/nf-core/blast/tblastn/main.nf index a5b9e9ef3b6..617864955c4 100644 --- a/modules/nf-core/blast/tblastn/main.nf +++ b/modules/nf-core/blast/tblastn/main.nf @@ -6,7 +6,6 @@ process BLAST_TBLASTN { def container_image = "blast:2.12.0--pl5262h3289130_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path db diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 83af7b58777..9b9be67296b 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -6,7 +6,6 @@ process BOWTIE2_ALIGN { def container_image = "mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 95e1819e624..487745671f0 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -6,7 +6,6 @@ process BOWTIE2_BUILD { def container_image = "bowtie2:2.4.4--py39hbb4e92a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index 894ce014b2a..d275b35b53a 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -8,7 +8,6 @@ process BRACKEN_BRACKEN { def container_image = "bracken:2.7--py39hc16433a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(kraken_report) path database diff --git a/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/modules/nf-core/bracken/combinebrackenoutputs/main.nf index 825c1b02ad8..a18fc6d4545 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -5,7 +5,6 @@ process BRACKEN_COMBINEBRACKENOUTPUTS { def container_image = "bracken:2.7--py39hc16433a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path input diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf index 3d6af2f93bc..fad2e3e64bf 100644 --- a/modules/nf-core/busco/main.nf +++ b/modules/nf-core/busco/main.nf @@ -6,7 +6,6 @@ process BUSCO { def container_image = "busco:5.4.3--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path('tmp_input/*') val lineage // Required: lineage to check against, "auto" enables --auto-lineage instead diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 68df053560e..68e82bd94d0 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -6,7 +6,6 @@ process BWA_ALN { def container_image = "bwa:0.7.17--h5bf99c6_8" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 059264dde20..02aff71b5d6 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -6,7 +6,6 @@ process BWA_INDEX { def container_image = "bwa:0.7.17--hed695b0_7" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 8dd91f17ff7..9ed32ffd3a0 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -6,7 +6,6 @@ process BWA_MEM { def container_image = "mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index ba7079bc943..4c5272553c5 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -6,7 +6,6 @@ process BWA_SAMPE { def container_image = "mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), path(sai) path index diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 9288d3e5ad7..ae27b055670 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -6,7 +6,6 @@ process BWA_SAMSE { def container_image = "mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), path(sai) path index diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index 3c6f581535e..2982fe20288 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -6,7 +6,6 @@ process BWAMEM2_INDEX { def container_image = "bwa-mem2:2.2.1--he513fc3_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 2937601dd8a..ffbdd4c3e95 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -6,7 +6,6 @@ process BWAMEM2_MEM { def container_image = "mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) tuple val(meta2), path(index) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index e81fcf8060c..d1f1494da97 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -6,7 +6,6 @@ process BWAMETH_ALIGN { def container_image = "bwameth:0.2.2--py_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 733e622783d..c83aef091f0 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -6,7 +6,6 @@ process BWAMETH_INDEX { def container_image = "bwameth:0.2.2--py_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta, stageAs: "bwameth/*" diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index ef103fa8417..7b28b17e019 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -6,7 +6,6 @@ process CAT_CAT { def container_image = "pigz:2.3.4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 44aea437a90..39ffde4ace2 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -6,7 +6,6 @@ process CAT_FASTQ { def container_image = "ubuntu:20.04" container [ params.container_registry ?: '' , container_image ].join('/') - input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index d3b45c597df..8d2a4d33dad 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -6,7 +6,6 @@ process CENTRIFUGE_CENTRIFUGE { def container_image = "centrifuge:1.0.4_beta--h9a82719_6" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path db diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index b947befa973..fc0067e5af3 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -6,7 +6,6 @@ process CENTRIFUGE_KREPORT { def container_image = "centrifuge:1.0.4_beta--h9a82719_6" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) path db diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index f9e8fe7e977..5ffdcac5ad6 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -6,7 +6,6 @@ process CHECKM_LINEAGEWF { def container_image = "checkm-genome:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) val fasta_ext diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index 69ba63b73f0..113c149ade0 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -6,7 +6,6 @@ process CHECKM_QA { def container_image = "checkm-genome:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file) path exclude_marker_file diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index a88f8d50d14..e768ff177fe 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -6,7 +6,6 @@ process CHROMAP_CHROMAP { def container_image = "mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path fasta diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 375b196ed1c..61646d37db7 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -6,7 +6,6 @@ process CHROMAP_INDEX { def container_image = "chromap:0.2.1--hd03093a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/clonalframeml/main.nf b/modules/nf-core/clonalframeml/main.nf index 11f9668f8fa..5a567d28fc4 100644 --- a/modules/nf-core/clonalframeml/main.nf +++ b/modules/nf-core/clonalframeml/main.nf @@ -6,7 +6,6 @@ process CLONALFRAMEML { def container_image = "clonalframeml:1.12--h7d875b9_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(newick), path(msa) diff --git a/modules/nf-core/cmseq/polymut/main.nf b/modules/nf-core/cmseq/polymut/main.nf index e48cd7eb459..d7c7378ee7b 100644 --- a/modules/nf-core/cmseq/polymut/main.nf +++ b/modules/nf-core/cmseq/polymut/main.nf @@ -7,7 +7,6 @@ process CMSEQ_POLYMUT { def container_image = "cmseq:1.0.4--pyhb7b1952_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(gff), path(fasta) diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index b0d8e1f667e..3c7c02d4108 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -6,7 +6,6 @@ process CNVKIT_ANTITARGET { def container_image = "cnvkit:0.9.9--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 251e81df21b..2255dbab2d0 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -6,7 +6,6 @@ process CNVKIT_BATCH { def container_image = "mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(tumor), path(normal) path fasta diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index 3dbc3b832fb..35eb6d21859 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -6,7 +6,6 @@ process CNVKIT_REFERENCE { def container_image = "cnvkit:0.9.9--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path targets diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf index d2303b8b5a0..4398b7381c8 100644 --- a/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -6,7 +6,6 @@ process CNVPYTOR_CALLCNVS { def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pytor) val bin_sizes diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf index c73dc3f006b..9cf6349401f 100644 --- a/modules/nf-core/cnvpytor/histogram/main.nf +++ b/modules/nf-core/cnvpytor/histogram/main.nf @@ -6,12 +6,10 @@ process CNVPYTOR_HISTOGRAM { def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pytor) val bin_sizes - output: tuple val(meta), path("${pytor.baseName}.pytor") , emit: pytor path "versions.yml" , emit: versions diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf index ad3ec0420bd..48cf4247869 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -6,7 +6,6 @@ process CNVPYTOR_IMPORTREADDEPTH { def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_file), path(index) path fasta diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf index b89c8e07804..d0beca6155c 100644 --- a/modules/nf-core/cnvpytor/partition/main.nf +++ b/modules/nf-core/cnvpytor/partition/main.nf @@ -6,7 +6,6 @@ process CNVPYTOR_PARTITION { def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pytor) val bin_sizes diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf index abe3a354c8b..cc6a3657611 100644 --- a/modules/nf-core/cnvpytor/view/main.nf +++ b/modules/nf-core/cnvpytor/view/main.nf @@ -6,7 +6,6 @@ process CNVPYTOR_VIEW { def container_image = "cnvpytor:1.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pytor_files) val bin_sizes diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index 3c15400d4df..000547856d4 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -6,7 +6,6 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { def container_image = "control-freec:11.6--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(cnvs), path(ratio) diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf index 130106ef791..e72914b9de5 100644 --- a/modules/nf-core/controlfreec/freec/main.nf +++ b/modules/nf-core/controlfreec/freec/main.nf @@ -6,7 +6,6 @@ process CONTROLFREEC_FREEC { def container_image = "control-freec:11.6--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) path fasta diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf index c9ed01a7991..7e3cc63a8b0 100644 --- a/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/modules/nf-core/controlfreec/freec2bed/main.nf @@ -6,7 +6,6 @@ process CONTROLFREEC_FREEC2BED { def container_image = "control-freec:11.6--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf index 367b4094534..a6a7391c203 100644 --- a/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/modules/nf-core/controlfreec/freec2circos/main.nf @@ -6,7 +6,6 @@ process CONTROLFREEC_FREEC2CIRCOS { def container_image = "control-freec:11.6--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ratio) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index 743e650dcc5..a0efd4cb61e 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -6,7 +6,6 @@ process CONTROLFREEC_MAKEGRAPH { def container_image = "control-freec:11.6--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ratio), path(baf) diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf index 751ed796acd..8319201ad6a 100644 --- a/modules/nf-core/cooler/cload/main.nf +++ b/modules/nf-core/cooler/cload/main.nf @@ -6,7 +6,6 @@ process COOLER_CLOAD { def container_image = "cooler:0.8.11--pyh3252c3a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pairs), path(index) val cool_bin diff --git a/modules/nf-core/cooler/digest/main.nf b/modules/nf-core/cooler/digest/main.nf index 15ebb7659e5..ebf4c246268 100644 --- a/modules/nf-core/cooler/digest/main.nf +++ b/modules/nf-core/cooler/digest/main.nf @@ -6,7 +6,6 @@ process COOLER_DIGEST { def container_image = "cooler:0.8.11--pyh3252c3a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path chromsizes diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf index 33a075a197c..83ee55a4adc 100644 --- a/modules/nf-core/cooler/dump/main.nf +++ b/modules/nf-core/cooler/dump/main.nf @@ -6,7 +6,6 @@ process COOLER_DUMP { def container_image = "cooler:0.8.11--pyh3252c3a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(cool) val resolution diff --git a/modules/nf-core/cooler/merge/main.nf b/modules/nf-core/cooler/merge/main.nf index 0ae64fdb9cd..25a5023ecd3 100644 --- a/modules/nf-core/cooler/merge/main.nf +++ b/modules/nf-core/cooler/merge/main.nf @@ -6,7 +6,6 @@ process COOLER_MERGE { def container_image = "cooler:0.8.11--pyh3252c3a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(cool) diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf index 39a128f5665..27ad949e641 100644 --- a/modules/nf-core/cooler/zoomify/main.nf +++ b/modules/nf-core/cooler/zoomify/main.nf @@ -6,7 +6,6 @@ process COOLER_ZOOMIFY { def container_image = "cooler:0.8.11--pyh3252c3a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(cool) diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index d8a3a4fcaee..e4554a46df6 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -6,7 +6,6 @@ process CRUMBLE { def container_image = "crumble:0.9.0--hb0d9459_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 1ba8f7b6004..d4cbe3efb60 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -6,7 +6,6 @@ process CSVTK_CONCAT { def container_image = "csvtk:0.23.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(csv) val in_format diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index 70766855f35..35c93df3f96 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -6,7 +6,6 @@ process CSVTK_SPLIT { def container_image = "csvtk:0.23.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(csv) val in_format diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebe91c8d39b..6e48cb42fa3 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -6,7 +6,6 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { def container_image = "multiqc:1.13--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path versions diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 6007e5e278c..f6eacb08ea2 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -6,7 +6,6 @@ process CUSTOM_GETCHROMSIZES { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf index 4b7a3faebce..fa01a3d72da 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -6,7 +6,6 @@ process CUSTOM_SRATOOLSNCBISETTINGS { def container_image = "sra-tools:2.11.0--pl5321ha49a11a_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - output: path('*.mkfg') , emit: ncbi_settings path 'versions.yml', emit: versions diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 0001f6dfd12..6da562270f0 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -6,7 +6,6 @@ process CUTADAPT { def container_image = "cutadapt:3.4--py39h38f01e4_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/damageprofiler/main.nf b/modules/nf-core/damageprofiler/main.nf index d3dd3afda34..ccc664d3c88 100644 --- a/modules/nf-core/damageprofiler/main.nf +++ b/modules/nf-core/damageprofiler/main.nf @@ -6,7 +6,6 @@ process DAMAGEPROFILER { def container_image = "damageprofiler:1.1--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf index bc3d6442147..4910197b872 100644 --- a/modules/nf-core/dastool/dastool/main.nf +++ b/modules/nf-core/dastool/dastool/main.nf @@ -6,7 +6,6 @@ process DASTOOL_DASTOOL { def container_image = "das_tool:1.1.4--r41hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(contigs), path(bins) path(proteins) diff --git a/modules/nf-core/dastool/fastatocontig2bin/main.nf b/modules/nf-core/dastool/fastatocontig2bin/main.nf index 247129c205a..71476df2bed 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -6,7 +6,6 @@ process DASTOOL_FASTATOCONTIG2BIN { def container_image = "das_tool:1.1.4--r41hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) val(extension) diff --git a/modules/nf-core/dastool/scaffolds2bin/main.nf b/modules/nf-core/dastool/scaffolds2bin/main.nf index 5f432d8b1f3..5f2644308c1 100644 --- a/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -6,7 +6,6 @@ process DASTOOL_SCAFFOLDS2BIN { def container_image = "das_tool:1.1.3--r41hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) val(extension) diff --git a/modules/nf-core/dedup/main.nf b/modules/nf-core/dedup/main.nf index 2516897ce65..c4f69c5f91b 100644 --- a/modules/nf-core/dedup/main.nf +++ b/modules/nf-core/dedup/main.nf @@ -6,7 +6,6 @@ process DEDUP { def container_image = "dedup:0.12.8--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index 74a1c347910..6169bb30823 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -11,7 +11,6 @@ process DEEPARG_DOWNLOADDATA { */ containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' } - input: output: diff --git a/modules/nf-core/deepbgc/download/main.nf b/modules/nf-core/deepbgc/download/main.nf index d7fde0fa9f2..01fe2cfd4e8 100644 --- a/modules/nf-core/deepbgc/download/main.nf +++ b/modules/nf-core/deepbgc/download/main.nf @@ -5,7 +5,6 @@ process DEEPBGC_DOWNLOAD { def container_image = "deepbgc:0.1.30--pyhb7b1952_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - output: path "deepbgc_db/" , emit: db path "versions.yml" , emit: versions diff --git a/modules/nf-core/deepbgc/pipeline/main.nf b/modules/nf-core/deepbgc/pipeline/main.nf index d56d4e66a6b..6889ad8eda2 100644 --- a/modules/nf-core/deepbgc/pipeline/main.nf +++ b/modules/nf-core/deepbgc/pipeline/main.nf @@ -6,7 +6,6 @@ process DEEPBGC_PIPELINE { def container_image = "deepbgc:0.1.30--pyhb7b1952_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(genome) path(db) diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 2581fa4c5f9..151d92c16e4 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -6,7 +6,6 @@ process DEEPTOOLS_BAMCOVERAGE { def container_image = "mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index) path(fasta) diff --git a/modules/nf-core/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf index b7b5fa2d80c..f236dc82d23 100644 --- a/modules/nf-core/deeptools/computematrix/main.nf +++ b/modules/nf-core/deeptools/computematrix/main.nf @@ -6,7 +6,6 @@ process DEEPTOOLS_COMPUTEMATRIX { def container_image = "deeptools:3.5.1--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bigwig) path bed diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf index fc866886d30..bd8d110a262 100644 --- a/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -6,7 +6,6 @@ process DEEPTOOLS_PLOTFINGERPRINT { def container_image = "deeptools:3.5.1--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf index e9066f99c46..43c32683a3f 100644 --- a/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/modules/nf-core/deeptools/plotheatmap/main.nf @@ -6,7 +6,6 @@ process DEEPTOOLS_PLOTHEATMAP { def container_image = "deeptools:3.5.1--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deeptools/plotprofile/main.nf b/modules/nf-core/deeptools/plotprofile/main.nf index 138bebc4cf4..51ac16e89cb 100644 --- a/modules/nf-core/deeptools/plotprofile/main.nf +++ b/modules/nf-core/deeptools/plotprofile/main.nf @@ -6,7 +6,6 @@ process DEEPTOOLS_PLOTPROFILE { def container_image = "deeptools:3.5.1--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(matrix) diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 344fdb030a7..663c852a233 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -2,7 +2,6 @@ process DEEPVARIANT { tag "$meta.id" label 'process_medium' - if (params.enable_conda) { exit 1, "Conda environments cannot be used with DeepVariant at the moment. Please use Docker or Singularity containers." } diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf index fc1fe06638f..b6b0368154e 100644 --- a/modules/nf-core/delly/call/main.nf +++ b/modules/nf-core/delly/call/main.nf @@ -6,7 +6,6 @@ process DELLY_CALL { def container_image = "delly:1.1.5--h358d541_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(exclude_bed) path fasta diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index b80cf19035b..9d104fbb7ba 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -6,7 +6,6 @@ process DIAMOND_BLASTP { def container_image = "diamond:2.0.15--hb97b32f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path db diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf index 6598e4d01a3..1cb19009d96 100644 --- a/modules/nf-core/diamond/blastx/main.nf +++ b/modules/nf-core/diamond/blastx/main.nf @@ -6,7 +6,6 @@ process DIAMOND_BLASTX { def container_image = "diamond:2.0.15--hb97b32f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path db diff --git a/modules/nf-core/diamond/makedb/main.nf b/modules/nf-core/diamond/makedb/main.nf index 91d5c88ecb0..d30f8cb1b1a 100644 --- a/modules/nf-core/diamond/makedb/main.nf +++ b/modules/nf-core/diamond/makedb/main.nf @@ -6,7 +6,6 @@ process DIAMOND_MAKEDB { def container_image = "diamond:2.0.15--hb97b32f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf index ea70899eda0..0b5fca67973 100644 --- a/modules/nf-core/dragmap/align/main.nf +++ b/modules/nf-core/dragmap/align/main.nf @@ -6,7 +6,6 @@ process DRAGMAP_ALIGN { def container_image = "mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path hashmap diff --git a/modules/nf-core/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf index 3cb527fd11d..a2c5393fdcb 100644 --- a/modules/nf-core/dragmap/hashtable/main.nf +++ b/modules/nf-core/dragmap/hashtable/main.nf @@ -6,7 +6,6 @@ process DRAGMAP_HASHTABLE { def container_image = "dragmap:1.2.1--hd4ca14e_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/dragonflye/main.nf b/modules/nf-core/dragonflye/main.nf index 90ed9f6baf7..1ed488b09cc 100644 --- a/modules/nf-core/dragonflye/main.nf +++ b/modules/nf-core/dragonflye/main.nf @@ -6,7 +6,6 @@ process DRAGONFLYE { def container_image = "dragonflye:1.0.11--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/dshbio/exportsegments/main.nf b/modules/nf-core/dshbio/exportsegments/main.nf index 19a3c6ca333..168411c9cc0 100644 --- a/modules/nf-core/dshbio/exportsegments/main.nf +++ b/modules/nf-core/dshbio/exportsegments/main.nf @@ -6,7 +6,6 @@ process DSHBIO_EXPORTSEGMENTS { def container_image = "dsh-bio:2.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/dshbio/filterbed/main.nf b/modules/nf-core/dshbio/filterbed/main.nf index 2f3c6fe5298..aff87336cc0 100644 --- a/modules/nf-core/dshbio/filterbed/main.nf +++ b/modules/nf-core/dshbio/filterbed/main.nf @@ -6,7 +6,6 @@ process DSHBIO_FILTERBED { def container_image = "dsh-bio:2.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/filtergff3/main.nf b/modules/nf-core/dshbio/filtergff3/main.nf index 2e317fb6c5e..c85b2b56566 100644 --- a/modules/nf-core/dshbio/filtergff3/main.nf +++ b/modules/nf-core/dshbio/filtergff3/main.nf @@ -6,7 +6,6 @@ process DSHBIO_FILTERGFF3 { def container_image = "dsh-bio:2.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/dshbio/splitbed/main.nf b/modules/nf-core/dshbio/splitbed/main.nf index 2452eb1736b..ee84e9e857e 100644 --- a/modules/nf-core/dshbio/splitbed/main.nf +++ b/modules/nf-core/dshbio/splitbed/main.nf @@ -6,7 +6,6 @@ process DSHBIO_SPLITBED { def container_image = "dsh-bio:2.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) diff --git a/modules/nf-core/dshbio/splitgff3/main.nf b/modules/nf-core/dshbio/splitgff3/main.nf index 1cb7c12e78f..54011ef00e5 100644 --- a/modules/nf-core/dshbio/splitgff3/main.nf +++ b/modules/nf-core/dshbio/splitgff3/main.nf @@ -6,7 +6,6 @@ process DSHBIO_SPLITGFF3 { def container_image = "dsh-bio:2.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gff3) diff --git a/modules/nf-core/ectyper/main.nf b/modules/nf-core/ectyper/main.nf index 123ea9323ab..9512c7d059c 100644 --- a/modules/nf-core/ectyper/main.nf +++ b/modules/nf-core/ectyper/main.nf @@ -6,7 +6,6 @@ process ECTYPER { def container_image = "ectyper:1.0.0--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index 2ef4d91700f..9cc6778ab96 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -6,7 +6,6 @@ process ELPREP_FILTER { def container_image = "elprep:5.1.2--he881be0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) val(run_haplotypecaller) @@ -21,7 +20,6 @@ process ELPREP_FILTER { val(get_activity_profile) val(get_assembly_regions) - output: tuple val(meta), path("output/**.{bam,sam}") ,emit: bam tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics diff --git a/modules/nf-core/elprep/merge/main.nf b/modules/nf-core/elprep/merge/main.nf index 225ff61efab..c1f934a80ca 100644 --- a/modules/nf-core/elprep/merge/main.nf +++ b/modules/nf-core/elprep/merge/main.nf @@ -6,7 +6,6 @@ process ELPREP_MERGE { def container_image = "elprep:5.1.2--he881be0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/elprep/split/main.nf b/modules/nf-core/elprep/split/main.nf index a48a961c30e..f8c12464565 100644 --- a/modules/nf-core/elprep/split/main.nf +++ b/modules/nf-core/elprep/split/main.nf @@ -6,7 +6,6 @@ process ELPREP_SPLIT { def container_image = "elprep:5.1.2--he881be0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/emboss/seqret/main.nf b/modules/nf-core/emboss/seqret/main.nf index 9c6ff155189..c3854527b05 100644 --- a/modules/nf-core/emboss/seqret/main.nf +++ b/modules/nf-core/emboss/seqret/main.nf @@ -6,7 +6,6 @@ process EMBOSS_SEQRET { def container_image = "emboss:6.6.0--hf657eab_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(sequence) val out_ext diff --git a/modules/nf-core/emmtyper/main.nf b/modules/nf-core/emmtyper/main.nf index 018c0fca675..ed094fc7052 100644 --- a/modules/nf-core/emmtyper/main.nf +++ b/modules/nf-core/emmtyper/main.nf @@ -6,7 +6,6 @@ process EMMTYPER { def container_image = "emmtyper:0.2.0--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/endorspy/main.nf b/modules/nf-core/endorspy/main.nf index 9730ee7a554..37b229305b0 100644 --- a/modules/nf-core/endorspy/main.nf +++ b/modules/nf-core/endorspy/main.nf @@ -6,7 +6,6 @@ process ENDORSPY { def container_image = "endorspy:0.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(stats), path(stats_optional) diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf index 8e58e386151..1fd084b6609 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/main.nf @@ -6,7 +6,6 @@ process ENSEMBLVEP { def container_image = "ensembl-vep:106.1--pl5321h4a94de4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) val genome @@ -51,7 +50,6 @@ process ENSEMBLVEP { --fork $task.cpus \\ --stats_file ${prefix}.summary.html \\ - cat <<-END_VERSIONS > versions.yml "${task.process}": ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') diff --git a/modules/nf-core/entrezdirect/esearch/main.nf b/modules/nf-core/entrezdirect/esearch/main.nf index ece9777bd0f..bec766670c2 100644 --- a/modules/nf-core/entrezdirect/esearch/main.nf +++ b/modules/nf-core/entrezdirect/esearch/main.nf @@ -6,7 +6,6 @@ process ENTREZDIRECT_ESEARCH { def container_image = "entrez-direct:16.2--he881be0_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), val(term) val database diff --git a/modules/nf-core/entrezdirect/esummary/main.nf b/modules/nf-core/entrezdirect/esummary/main.nf index c7c706c5ec6..b8234d6027d 100644 --- a/modules/nf-core/entrezdirect/esummary/main.nf +++ b/modules/nf-core/entrezdirect/esummary/main.nf @@ -6,7 +6,6 @@ process ENTREZDIRECT_ESUMMARY { def container_image = "entrez-direct:16.2--he881be0_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), val(uid), path(uids_file) val database diff --git a/modules/nf-core/entrezdirect/xtract/main.nf b/modules/nf-core/entrezdirect/xtract/main.nf index f0f3d0c4a51..f4e68f169ee 100644 --- a/modules/nf-core/entrezdirect/xtract/main.nf +++ b/modules/nf-core/entrezdirect/xtract/main.nf @@ -6,7 +6,6 @@ process ENTREZDIRECT_XTRACT { def container_image = "entrez-direct:16.2--he881be0_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(xml_input) val pattern diff --git a/modules/nf-core/epang/main.nf b/modules/nf-core/epang/main.nf index 63ec9486044..00fe006be80 100644 --- a/modules/nf-core/epang/main.nf +++ b/modules/nf-core/epang/main.nf @@ -6,7 +6,6 @@ process EPANG { def container_image = "epa-ng:0.3.8--h9a82719_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(queryaln) path referencealn diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index dfe32feed47..8373e6930cc 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -6,7 +6,6 @@ process EXPANSIONHUNTER { def container_image = "expansionhunter:4.0.2--he785bd8_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path fasta diff --git a/modules/nf-core/falco/main.nf b/modules/nf-core/falco/main.nf index 16881624da5..670caeaf7e9 100644 --- a/modules/nf-core/falco/main.nf +++ b/modules/nf-core/falco/main.nf @@ -2,7 +2,6 @@ process FALCO { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::falco=1.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3': diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf index a1d7288a7b3..f3a698d16bb 100644 --- a/modules/nf-core/faqcs/main.nf +++ b/modules/nf-core/faqcs/main.nf @@ -6,7 +6,6 @@ process FAQCS { def container_image = "faqcs:2.10--r41h9a82719_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) @@ -38,7 +37,6 @@ process FAQCS { $args \\ 2> ${prefix}.fastp.log - if [[ -f ${prefix}.unpaired.trimmed.fastq ]]; then mv ${prefix}.unpaired.trimmed.fastq ${prefix}.trimmed.fastq gzip ${prefix}.trimmed.fastq diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf index 77b14aef3c4..3968dc3c504 100644 --- a/modules/nf-core/fargene/main.nf +++ b/modules/nf-core/fargene/main.nf @@ -7,7 +7,6 @@ process FARGENE { def container_image = "fargene:0.1--py27h21c881e_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag tuple val(meta), path(input) diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf index fd75cde9c41..05e6229572b 100644 --- a/modules/nf-core/fastani/main.nf +++ b/modules/nf-core/fastani/main.nf @@ -6,7 +6,6 @@ process FASTANI { def container_image = "fastani:1.32--he1c1bb9_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(query) path reference diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index 37c3d23ac0f..a71293f11d9 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -6,7 +6,6 @@ process FASTAWINDOWS { def container_image = "fasta_windows:0.2.4--hec16e2b_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index e11226c2301..1c3d9e38cf2 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -6,7 +6,6 @@ process FASTP { def container_image = "fastp:0.23.2--h79da9fb_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) val save_trimmed_fail diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index fa7787e2570..5cc97fc0dc9 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -6,7 +6,6 @@ process FASTQC { def container_image = "fastqc:0.11.9--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqscan/main.nf b/modules/nf-core/fastqscan/main.nf index 2d437465454..d122c86403b 100644 --- a/modules/nf-core/fastqscan/main.nf +++ b/modules/nf-core/fastqscan/main.nf @@ -6,7 +6,6 @@ process FASTQSCAN { def container_image = "fastq-scan:0.4.4--h7d875b9_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fasttree/main.nf b/modules/nf-core/fasttree/main.nf index 305340ca068..9203a577306 100644 --- a/modules/nf-core/fasttree/main.nf +++ b/modules/nf-core/fasttree/main.nf @@ -5,7 +5,6 @@ process FASTTREE { def container_image = "fasttree:2.1.10--h516909a_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path alignment diff --git a/modules/nf-core/ffq/main.nf b/modules/nf-core/ffq/main.nf index 98c23a1e30a..3fdc225bcf8 100644 --- a/modules/nf-core/ffq/main.nf +++ b/modules/nf-core/ffq/main.nf @@ -6,7 +6,6 @@ process FFQ { def container_image = "ffq:0.2.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: val ids diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 9ddfa9c32f0..9bf36895ec6 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -6,7 +6,6 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { def container_image = "fgbio:2.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index 09a389fd8a1..2d6afab3d90 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -6,7 +6,6 @@ process FGBIO_FASTQTOBAM { def container_image = "fgbio:2.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index 1bcc28fcbee..ce09192424d 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -6,7 +6,6 @@ process FGBIO_GROUPREADSBYUMI { def container_image = "fgbio:2.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(taggedbam) val(strategy) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index 62f1dd290be..1b4241591d7 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -6,7 +6,6 @@ process FGBIO_SORTBAM { def container_image = "fgbio:2.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 1cacdfe26bc..23337d9a7a2 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -6,7 +6,6 @@ process FGBIO_ZIPPERBAMS { def container_image = "fgbio:2.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(unmapped_bam) tuple val(meta), path(mapped_bam) @@ -48,7 +47,6 @@ process FGBIO_ZIPPERBAMS { ${args} \\ --output ${prefix}.bam - cat <<-END_VERSIONS > versions.yml "${task.process}": fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//') diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index 0aa33f1aee8..29348b2eaa4 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -6,7 +6,6 @@ process FILTLONG { def container_image = "filtlong:0.2.1--h9a82719_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index c13639c423f..4a082d54d32 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -5,7 +5,6 @@ process FLASH { def container_image = "flash:1.2.11--hed695b0_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index a307f6f199d..7f607270862 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -6,7 +6,6 @@ process FLYE { def container_image = "flye:2.9--py39h6935b12_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) val mode diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf index cf17aa29c11..c61fc409d4c 100644 --- a/modules/nf-core/fq/lint/main.nf +++ b/modules/nf-core/fq/lint/main.nf @@ -6,7 +6,6 @@ process FQ_LINT { def container_image = "fq:0.9.1--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/freebayes/main.nf b/modules/nf-core/freebayes/main.nf index 92839ce71ac..97357440cfc 100644 --- a/modules/nf-core/freebayes/main.nf +++ b/modules/nf-core/freebayes/main.nf @@ -6,7 +6,6 @@ process FREEBAYES { def container_image = "freebayes:1.3.5--py38ha193a2f_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) path fasta diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index b4dabfb870b..b1189dbbcec 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -8,7 +8,6 @@ process GAMMA_GAMMA { def container_image = "gamma:2.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path(db) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 9f20e2689fc..f677803f0f3 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -6,7 +6,6 @@ process GAPPA_EXAMINEASSIGN { def container_image = "gappa:0.8.0--h9a82719_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(jplace) path taxonomy diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index 82aa13f96e8..8bd6e088de5 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -6,7 +6,6 @@ process GAPPA_EXAMINEGRAFT { def container_image = "gappa:0.8.0--h9a82719_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 2f20d14174e..5f761c696fd 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -6,7 +6,6 @@ process GAPPA_EXAMINEHEATTREE { def container_image = "gappa:0.8.0--h9a82719_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 10bf2920306..8499081578d 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -6,7 +6,6 @@ process GATK_INDELREALIGNER { def container_image = "gatk:3.5--hdfd78af_11" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(intervals) path(fasta) diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index 821bde8c202..82b3082c5f3 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -6,7 +6,6 @@ process GATK_REALIGNERTARGETCREATOR { def container_image = "gatk:3.5--hdfd78af_11" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(index) path fasta diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index 0e03603b4d9..90fac356ed1 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -6,7 +6,6 @@ process GATK_UNIFIEDGENOTYPER { def container_image = "gatk:3.5--hdfd78af_11" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(index) path fasta diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 89460fd093b..9a0ee5122a7 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -6,7 +6,6 @@ process GATK4_APPLYBQSR { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 6b2d1f138bb..0eb1da91854 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -6,7 +6,6 @@ process GATK4_APPLYVQSR { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) path fasta diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index d55030eec31..a986e8bafd2 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -6,7 +6,6 @@ process GATK4_BASERECALIBRATOR { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index ea26dbb6963..20e6f752295 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -6,7 +6,6 @@ process GATK4_BEDTOINTERVALLIST { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path dict diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index ad25dfe4824..d0d7593d4c4 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -6,7 +6,6 @@ process GATK4_CALCULATECONTAMINATION { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 22d4c5e087d..9ccc9ed02b4 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -6,7 +6,6 @@ process GATK4_CALIBRATEDRAGSTRMODEL { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bam_index), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index eea51855c4b..beffc26cf6b 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -6,7 +6,6 @@ process GATK4_COLLECTREADCOUNTS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(intervals) path(fasta) diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 511fcd5db24..8bb0951f87e 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -6,7 +6,6 @@ process GATK4_COLLECTSVEVIDENCE { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi) path fasta diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 45b777f2e44..1e54200b285 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -6,7 +6,6 @@ process GATK4_COMBINEGVCFS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(vcf_idx) path fasta diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 6158185c746..d5b8c452abd 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -6,7 +6,6 @@ process GATK4_COMPOSESTRTABLEFILE { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path(fasta) path(fasta_fai) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 89c4181d876..9e3edfcb24a 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -6,7 +6,6 @@ process GATK4_CREATESEQUENCEDICTIONARY { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 9fa188ed314..5dc3e503638 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -6,7 +6,6 @@ process GATK4_CREATESOMATICPANELOFNORMALS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(genomicsdb) path fasta diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 5b755ae9a55..9ade02c550c 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -6,7 +6,6 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) path fasta diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 275ee3f1507..81ac430259b 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -6,7 +6,6 @@ process GATK4_FASTQTOSAM { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index c9d33d72439..74652a7e503 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -6,7 +6,6 @@ process GATK4_FILTERMUTECTCALLS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) path fasta diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 16b9ca2872f..bf87479cdae 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -6,7 +6,6 @@ process GATK4_FILTERVARIANTTRANCHES { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi), path(intervals) path resources @@ -15,7 +14,6 @@ process GATK4_FILTERVARIANTTRANCHES { path fai path dict - output: tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index df18452a74b..2775676a789 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -6,7 +6,6 @@ process GATK4_GATHERBQSRREPORTS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 16a3e2e4e8c..fd4251ed196 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -6,8 +6,6 @@ process GATK4_GATHERPILEUPSUMMARIES { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - - input: tuple val(meta), path(pileup) path dict diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index ea469129019..ed03a1fafbe 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -6,7 +6,6 @@ process GATK4_GENOMICSDBIMPORT { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) val run_intlist diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index f66cd6c11fe..d49959b6cdb 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -6,7 +6,6 @@ process GATK4_GENOTYPEGVCFS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) path fasta diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index a3cf517a184..c6e01a3a45f 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -6,7 +6,6 @@ process GATK4_GETPILEUPSUMMARIES { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(index), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index b3633e9ea88..9ebac926304 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -6,7 +6,6 @@ process GATK4_HAPLOTYPECALLER { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) path fasta diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index f0460e476b1..c72acc95034 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -6,7 +6,6 @@ process GATK4_INDEXFEATUREFILE { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 48c356e610b..d08f6e7eaad 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -6,7 +6,6 @@ process GATK4_INTERVALLISTTOBED { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 882c19110ab..8dcc07c08b1 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -6,7 +6,6 @@ process GATK4_INTERVALLISTTOOLS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index 4ede9cb90dc..c8a8e91729c 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -6,7 +6,6 @@ process GATK4_LEARNREADORIENTATIONMODEL { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index cd1d40ab0ce..a3a346285ab 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -6,7 +6,6 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index bd2eeeb29c2..b49539a29f0 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -6,7 +6,6 @@ process GATK4_MARKDUPLICATES { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta @@ -44,7 +43,6 @@ process GATK4_MARKDUPLICATES { ${reference} \\ $args - if [[ ${prefix} == *.cram ]]; then mv ${prefix}.bai ${prefix}.crai fi diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf index b8c315fc3df..f9f8d75a829 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -24,7 +24,6 @@ process GATK4_MARKDUPLICATES_SPARK { prefix = task.ext.prefix ?: "${meta.id}" def input_list = bam.collect{"--input $it"}.join(' ') - def avail_mem = 3 if (!task.memory) { log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index a876930ef53..ffb983b814b 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -6,7 +6,6 @@ process GATK4_MERGEBAMALIGNMENT { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(aligned), path(unmapped) path fasta diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 17d7103b11b..b2dcd20aabd 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -6,7 +6,6 @@ process GATK4_MERGEMUTECTSTATS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index c42e2e29a4a..4e9477af8f4 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -6,7 +6,6 @@ process GATK4_MERGEVCFS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) path dict diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 45aaae61abb..03c75234814 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -6,7 +6,6 @@ process GATK4_MUTECT2 { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 4c7a2d4a676..3afe1e6fd78 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -6,7 +6,6 @@ process GATK4_PRINTSVEVIDENCE { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(evidence_files), path(evidence_indices) path bed diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index aa5222e7cc3..fe85d081057 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -6,7 +6,6 @@ process GATK4_REBLOCKGVCF { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gvcf), path(tbi), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index cd382e489f3..5b45381a432 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -6,7 +6,6 @@ process GATK4_REVERTSAM { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index e851f9163b2..f2e31d3949e 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -6,7 +6,6 @@ process GATK4_SAMTOFASTQ { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index b836d6d9366..64b6be4c6fa 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -6,7 +6,6 @@ process GATK4_SELECTVARIANTS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index 19fa0440632..9f828a190d9 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -6,7 +6,6 @@ process GATK4_SPLITINTERVALS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(intervals) path(fasta) diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index df3f23c3a57..250ebfce8bc 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -6,7 +6,6 @@ process GATK4_SPLITNCIGARREADS { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(intervals) path fasta diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 1665a3d4f94..9ed5daf4cf0 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -6,7 +6,6 @@ process GATK4_VARIANTFILTRATION { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) path fasta diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 37e1168061c..46009aa8570 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -6,7 +6,6 @@ process GATK4_VARIANTRECALIBRATOR { def container_image = "gatk4:4.2.6.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate path resource_vcf // resource vcf diff --git a/modules/nf-core/gecco/run/main.nf b/modules/nf-core/gecco/run/main.nf index a5e9bc74fcb..949a267f433 100644 --- a/modules/nf-core/gecco/run/main.nf +++ b/modules/nf-core/gecco/run/main.nf @@ -6,12 +6,10 @@ process GECCO_RUN { def container_image = "gecco:0.9.2--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(hmm) path model_dir - output: tuple val(meta), path("*.genes.tsv") , optional: true, emit: genes tuple val(meta), path("*.features.tsv") , emit: features diff --git a/modules/nf-core/genmap/index/main.nf b/modules/nf-core/genmap/index/main.nf index 66be4332470..561fbd6e958 100644 --- a/modules/nf-core/genmap/index/main.nf +++ b/modules/nf-core/genmap/index/main.nf @@ -6,7 +6,6 @@ process GENMAP_INDEX { def container_image = "genmap:1.3.0--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/genmap/mappability/main.nf b/modules/nf-core/genmap/mappability/main.nf index 2457a90aa67..21d0c516291 100644 --- a/modules/nf-core/genmap/mappability/main.nf +++ b/modules/nf-core/genmap/mappability/main.nf @@ -6,7 +6,6 @@ process GENMAP_MAPPABILITY { def container_image = "genmap:1.3.0--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path index diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index e831a936872..85514d16e7f 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -6,7 +6,6 @@ process GENMOD_ANNOTATE { def container_image = "genmod:3.7.4--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 3320c7c65be..a28a2226304 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -6,7 +6,6 @@ process GENMOD_COMPOUND { def container_image = "genmod:3.7.4--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 2c64fd656ce..f00c7eba8d3 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -6,7 +6,6 @@ process GENMOD_MODELS { def container_image = "genmod:3.7.4--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_vcf) path (fam) diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 4f019a78d47..01eec98e857 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -6,7 +6,6 @@ process GENMOD_SCORE { def container_image = "genmod:3.7.4--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_vcf) path (fam) diff --git a/modules/nf-core/genomescope2/main.nf b/modules/nf-core/genomescope2/main.nf index 85e09760949..459798df737 100644 --- a/modules/nf-core/genomescope2/main.nf +++ b/modules/nf-core/genomescope2/main.nf @@ -6,7 +6,6 @@ process GENOMESCOPE2 { def container_image = "genomescope2:2.0--py310r41hdfd78af_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(histogram) diff --git a/modules/nf-core/genotyphi/parse/main.nf b/modules/nf-core/genotyphi/parse/main.nf index d02cf9c6ed6..387d9bc4289 100644 --- a/modules/nf-core/genotyphi/parse/main.nf +++ b/modules/nf-core/genotyphi/parse/main.nf @@ -6,7 +6,6 @@ process GENOTYPHI_PARSE { def container_image = "genotyphi:1.9.1--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(json) diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf index 240d39a2472..b98fc447128 100644 --- a/modules/nf-core/genrich/main.nf +++ b/modules/nf-core/genrich/main.nf @@ -6,7 +6,6 @@ process GENRICH { def container_image = "genrich:0.6.1--h5bf99c6_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(treatment_bam) path control_bam diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index b6e4d018362..6313b3c2397 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -7,7 +7,6 @@ process GFAFFIX { def container_image = "gfaffix:0.1.4--hec16e2b_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 65b82714e8e..d8c80b144f5 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -6,7 +6,6 @@ process GFFREAD { def container_image = "gffread:0.12.1--h8b12597_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path gff diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf index f74aa64e014..dfe3e850cdf 100644 --- a/modules/nf-core/glimpse/chunk/main.nf +++ b/modules/nf-core/glimpse/chunk/main.nf @@ -6,7 +6,6 @@ process GLIMPSE_CHUNK { def container_image = "glimpse-bio:1.1.1--h2ce4488_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) val region diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 9cce169f0cf..bf9d562aa98 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -6,7 +6,6 @@ process GLNEXUS { def container_image = "glnexus:1.4.1--h40d77a6_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gvcfs) diff --git a/modules/nf-core/goat/taxonsearch/main.nf b/modules/nf-core/goat/taxonsearch/main.nf index c43751e46f3..845849019e7 100644 --- a/modules/nf-core/goat/taxonsearch/main.nf +++ b/modules/nf-core/goat/taxonsearch/main.nf @@ -6,7 +6,6 @@ process GOAT_TAXONSEARCH { def container_image = "goat:0.2.0--h92d785c_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), val(taxon), path(taxa_file) diff --git a/modules/nf-core/graphmap2/align/main.nf b/modules/nf-core/graphmap2/align/main.nf index 1b167b94844..25f3857d373 100644 --- a/modules/nf-core/graphmap2/align/main.nf +++ b/modules/nf-core/graphmap2/align/main.nf @@ -7,7 +7,6 @@ process GRAPHMAP2_ALIGN { def container_image = "graphmap:0.6.3--he513fc3_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path fasta diff --git a/modules/nf-core/graphmap2/index/main.nf b/modules/nf-core/graphmap2/index/main.nf index 6cec5822e8f..9e0d2cc09a0 100644 --- a/modules/nf-core/graphmap2/index/main.nf +++ b/modules/nf-core/graphmap2/index/main.nf @@ -5,7 +5,6 @@ process GRAPHMAP2_INDEX { def container_image = "graphmap:0.6.3--he513fc3_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index 0bf377c9fce..b06e054e395 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -6,7 +6,6 @@ process GSTAMA_COLLAPSE { def container_image = "gs-tama:1.0.3--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 542c9f1733b..77d6b44face 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -6,7 +6,6 @@ process GSTAMA_MERGE { def container_image = "gs-tama:1.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path filelist diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index 8b54a34e107..17ead669fc2 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -6,7 +6,6 @@ process GSTAMA_POLYACLEANUP { def container_image = "gs-tama:1.0.3--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index dc35a660ba3..9e828e9bef1 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -7,7 +7,6 @@ process GTDBTK_CLASSIFYWF { def container_image = "gtdbtk:1.5.0--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path("bins/*") tuple val(db_name), path("database/*") diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index dfd7e24aacf..e50cea94419 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -5,7 +5,6 @@ process GUBBINS { def container_image = "gubbins:3.0.0--py39h5bf99c6_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path alignment diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 39243699715..b520fd25fd4 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -6,7 +6,6 @@ process GUNC_DOWNLOADDB { def container_image = "gunc:1.0.5--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: val db_name diff --git a/modules/nf-core/gunc/run/main.nf b/modules/nf-core/gunc/run/main.nf index 1cd61c39fab..0729b1cf596 100644 --- a/modules/nf-core/gunc/run/main.nf +++ b/modules/nf-core/gunc/run/main.nf @@ -6,7 +6,6 @@ process GUNC_RUN { def container_image = "gunc:1.0.5--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path(db) diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 79cd51592f3..226119c188f 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -6,7 +6,6 @@ process GUNZIP { def container_image = "ubuntu:20.04" container [ params.container_registry ?: '' , container_image ].join('/') - input: tuple val(meta), path(archive) diff --git a/modules/nf-core/gvcftools/extractvariants/main.nf b/modules/nf-core/gvcftools/extractvariants/main.nf index 84f33cbf1e4..e843b6e2d05 100644 --- a/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/modules/nf-core/gvcftools/extractvariants/main.nf @@ -6,7 +6,6 @@ process GVCFTOOLS_EXTRACTVARIANTS { def container_image = "gvcftools:0.17.0--he941832_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gvcf) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index d8c1a738a28..18cf47c923c 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -6,7 +6,6 @@ process HAMRONIZATION_ABRICATE { def container_image = "hamronization:1.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) val(format) @@ -34,7 +33,6 @@ process HAMRONIZATION_ABRICATE { --reference_database_version ${reference_db_version} \\ > ${prefix}.${format} - cat <<-END_VERSIONS > versions.yml "${task.process}": hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index f3c59d63669..efb13a74145 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -6,7 +6,6 @@ process HAMRONIZATION_AMRFINDERPLUS { def container_image = "hamronization:1.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) val(format) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 7811354bcdb..9b629cc1c2d 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -6,7 +6,6 @@ process HAMRONIZATION_DEEPARG { def container_image = "hamronization:1.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) val(format) @@ -35,7 +34,6 @@ process HAMRONIZATION_DEEPARG { --input_file_name ${prefix} \\ > ${prefix}.${format} - cat <<-END_VERSIONS > versions.yml "${task.process}": hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index 48f31f55f47..f8aea6076c8 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -6,7 +6,6 @@ process HAMRONIZATION_FARGENE { def container_image = "hamronization:1.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) val(format) diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index 8360ddcadab..500ee22527c 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -6,7 +6,6 @@ process HAMRONIZATION_RGI { def container_image = "hamronization:1.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) val(format) diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index 20abd42258a..df67e6af826 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -5,7 +5,6 @@ process HAMRONIZATION_SUMMARIZE { def container_image = "hamronization:1.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path(reports) val(format) diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf index 3352ba56241..6268f77d327 100644 --- a/modules/nf-core/haplocheck/main.nf +++ b/modules/nf-core/haplocheck/main.nf @@ -6,7 +6,6 @@ process HAPLOCHECK { def container_image = "haplocheck:1.3.3--h4a94de4_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/haplogrep2/classify/main.nf b/modules/nf-core/haplogrep2/classify/main.nf index e15fdc1d42d..372e0390d26 100644 --- a/modules/nf-core/haplogrep2/classify/main.nf +++ b/modules/nf-core/haplogrep2/classify/main.nf @@ -6,7 +6,6 @@ process HAPLOGREP2_CLASSIFY { def container_image = "haplogrep:2.4.0--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(inputfile) val(format) diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf index 951b0db90bf..a54e9a5c777 100644 --- a/modules/nf-core/happy/happy/main.nf +++ b/modules/nf-core/happy/happy/main.nf @@ -7,7 +7,6 @@ process HAPPY_HAPPY { def container_image = "hap.py:0.3.14--py27h5c5a3ab_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(truth_vcf), path(query_vcf), path(bed) tuple path(fasta), path(fasta_fai) diff --git a/modules/nf-core/happy/prepy/main.nf b/modules/nf-core/happy/prepy/main.nf index 1c8f10333af..8141bc16dcf 100644 --- a/modules/nf-core/happy/prepy/main.nf +++ b/modules/nf-core/happy/prepy/main.nf @@ -7,7 +7,6 @@ process HAPPY_PREPY { def container_image = "hap.py:0.3.14--py27h5c5a3ab_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(bed) tuple path(fasta), path(fasta_fai) diff --git a/modules/nf-core/hicap/main.nf b/modules/nf-core/hicap/main.nf index 7e994bfaa85..5997540eafb 100644 --- a/modules/nf-core/hicap/main.nf +++ b/modules/nf-core/hicap/main.nf @@ -6,7 +6,6 @@ process HICAP { def container_image = "hicap:1.0.3--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path database_dir diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index ada1ea9a488..e1246fd1788 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -6,7 +6,6 @@ process HIFIASM { def container_image = "hifiasm:0.15.4--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path paternal_kmer_dump diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index bf5cc861745..aa816c23734 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -7,7 +7,6 @@ process HISAT2_ALIGN { def container_image = "mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index bf43c78c012..876ef0d7b11 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -8,7 +8,6 @@ process HISAT2_BUILD { def container_image = "hisat2:2.2.1--h1b792b2_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path gtf diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 0743728ab17..eeaf9f82266 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -7,7 +7,6 @@ process HISAT2_EXTRACTSPLICESITES { def container_image = "hisat2:2.2.1--h1b792b2_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path gtf diff --git a/modules/nf-core/hmmcopy/gccounter/main.nf b/modules/nf-core/hmmcopy/gccounter/main.nf index 8d9e1fc8bd2..da3a37b3d48 100644 --- a/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/modules/nf-core/hmmcopy/gccounter/main.nf @@ -6,7 +6,6 @@ process HMMCOPY_GCCOUNTER { def container_image = "hmmcopy:0.1.1--h2e03b76_7" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/hmmcopy/generatemap/main.nf b/modules/nf-core/hmmcopy/generatemap/main.nf index 8bef9f49ce5..524031fe8d3 100644 --- a/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/modules/nf-core/hmmcopy/generatemap/main.nf @@ -7,7 +7,6 @@ process HMMCOPY_GENERATEMAP { def container_image = "hmmcopy:0.1.1--h2e03b76_7" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/hmmcopy/mapcounter/main.nf b/modules/nf-core/hmmcopy/mapcounter/main.nf index eeadc58cc98..094b86673f2 100644 --- a/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -6,7 +6,6 @@ process HMMCOPY_MAPCOUNTER { def container_image = "hmmcopy:0.1.1--h2e03b76_7" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path bigwig diff --git a/modules/nf-core/hmmcopy/readcounter/main.nf b/modules/nf-core/hmmcopy/readcounter/main.nf index dd03d43dc34..95384e93e4c 100644 --- a/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/modules/nf-core/hmmcopy/readcounter/main.nf @@ -7,7 +7,6 @@ process HMMCOPY_READCOUNTER { def container_image = "hmmcopy:0.1.1--h2e03b76_7" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index b06d96c70e2..8940ad6d1c1 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -6,7 +6,6 @@ process HMMER_ESLALIMASK { def container_image = "hmmer:3.3.2--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) path maskfile diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 5b18e8245a0..0770d38467c 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -6,7 +6,6 @@ process HMMER_ESLREFORMAT { def container_image = "hmmer:3.3.2--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 3ffec25fe38..2a02bdd719f 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -6,7 +6,6 @@ process HMMER_HMMALIGN { def container_image = "hmmer:3.3.2--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path hmm diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index d8ab2b89baf..04ff45afd98 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -6,7 +6,6 @@ process HMMER_HMMBUILD { def container_image = "hmmer:3.3.2--h87f3376_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(alignment) path mxfile diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index 80ac421a2f3..745d919b5ac 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -6,7 +6,6 @@ process HMMER_HMMSEARCH { def container_image = "hmmer:3.3.2--h1b792b2_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain) diff --git a/modules/nf-core/hmtnote/main.nf b/modules/nf-core/hmtnote/main.nf index 1a2d7a13927..f80db0aba39 100644 --- a/modules/nf-core/hmtnote/main.nf +++ b/modules/nf-core/hmtnote/main.nf @@ -6,7 +6,6 @@ process HMTNOTE { def container_image = "hmtnote:0.7.2--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 2c9127f950a..474c9b2e264 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -7,7 +7,6 @@ process HOMER_ANNOTATEPEAKS { def container_image = "homer:4.11--pl526hc9558a2_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(peak) path fasta diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf index ba392fffccb..27de4a7408c 100644 --- a/modules/nf-core/homer/findpeaks/main.nf +++ b/modules/nf-core/homer/findpeaks/main.nf @@ -7,7 +7,6 @@ process HOMER_FINDPEAKS { def container_image = "homer:4.11--pl526hc9558a2_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/maketagdirectory/main.nf b/modules/nf-core/homer/maketagdirectory/main.nf index 96ce3e6024b..de37a1a6ef2 100644 --- a/modules/nf-core/homer/maketagdirectory/main.nf +++ b/modules/nf-core/homer/maketagdirectory/main.nf @@ -8,7 +8,6 @@ process HOMER_MAKETAGDIRECTORY { def container_image = "mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/homer/makeucscfile/main.nf b/modules/nf-core/homer/makeucscfile/main.nf index d722147035b..a1894f48254 100644 --- a/modules/nf-core/homer/makeucscfile/main.nf +++ b/modules/nf-core/homer/makeucscfile/main.nf @@ -7,7 +7,6 @@ process HOMER_MAKEUCSCFILE { def container_image = "homer:4.11--pl526hc9558a2_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(tagDir) diff --git a/modules/nf-core/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf index 8c02ca1c474..3727fa536f0 100644 --- a/modules/nf-core/homer/pos2bed/main.nf +++ b/modules/nf-core/homer/pos2bed/main.nf @@ -7,7 +7,6 @@ process HOMER_POS2BED { def container_image = "homer:4.11--pl526hc9558a2_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(peaks) diff --git a/modules/nf-core/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf index 5745568f251..8c5bd9de145 100644 --- a/modules/nf-core/hpsuissero/main.nf +++ b/modules/nf-core/hpsuissero/main.nf @@ -7,7 +7,6 @@ process HPSUISSERO { def container_image = "hpsuissero:1.0.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index a26dd46b7b5..9ecb194b483 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -6,7 +6,6 @@ process ICHORCNA_CREATEPON { def container_image = "r-ichorcna:0.3.2--r41hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path wigs path gc_wig diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index 6cbc5e61087..c831e35eba8 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -7,7 +7,6 @@ process ICHORCNA_RUN { def container_image = "r-ichorcna:0.3.2--r41hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(wig) path gc_wig diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index 691dba92fcc..87903a0e61f 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -6,7 +6,6 @@ process IDR { def container_image = "idr:2.0.4.2--py39hcbe4a3b_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path peaks val peak_type diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index 6b38736e1f3..efc08b7cfb9 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -6,7 +6,6 @@ process INSTRAIN_PROFILE { def container_image = "instrain:1.6.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path genome_fasta diff --git a/modules/nf-core/iqtree/main.nf b/modules/nf-core/iqtree/main.nf index cc9b128414a..3546de6923a 100644 --- a/modules/nf-core/iqtree/main.nf +++ b/modules/nf-core/iqtree/main.nf @@ -6,7 +6,6 @@ process IQTREE { def container_image = "iqtree:2.1.4_beta--hdcc8f71_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path alignment val constant_sites diff --git a/modules/nf-core/ismapper/main.nf b/modules/nf-core/ismapper/main.nf index e0e2925787e..413b6f46ac3 100644 --- a/modules/nf-core/ismapper/main.nf +++ b/modules/nf-core/ismapper/main.nf @@ -6,7 +6,6 @@ process ISMAPPER { def container_image = "ismapper:2.0.2--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), path(reference), path(query) diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq3/cluster/main.nf index dd8fc614f2d..c9fa0a537b9 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq3/cluster/main.nf @@ -6,7 +6,6 @@ process ISOSEQ3_CLUSTER { def container_image = "isoseq3:3.4.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf index be98d4029a9..d87998a130a 100644 --- a/modules/nf-core/isoseq3/refine/main.nf +++ b/modules/nf-core/isoseq3/refine/main.nf @@ -6,7 +6,6 @@ process ISOSEQ3_REFINE { def container_image = "isoseq3:3.4.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path primers diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 11156bf19c0..64572bcbdd9 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -6,7 +6,6 @@ process IVAR_CONSENSUS { def container_image = "ivar:1.3.1--h089eab3_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index c19f493a62b..6eb98abb62b 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -6,7 +6,6 @@ process IVAR_TRIM { def container_image = "ivar:1.3.1--h089eab3_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path bed diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 64d8d40d7fd..2dacc92bb06 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -6,7 +6,6 @@ process IVAR_VARIANTS { def container_image = "ivar:1.3.1--h089eab3_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/jupyternotebook/main.nf b/modules/nf-core/jupyternotebook/main.nf index 8b3640f436c..c43e2072d9c 100644 --- a/modules/nf-core/jupyternotebook/main.nf +++ b/modules/nf-core/jupyternotebook/main.nf @@ -11,7 +11,6 @@ process JUPYTERNOTEBOOK { def container_image = "mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(notebook) val parameters diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf index 37fc9c2b943..02c73f45773 100644 --- a/modules/nf-core/kaiju/kaiju/main.nf +++ b/modules/nf-core/kaiju/kaiju/main.nf @@ -6,7 +6,6 @@ process KAIJU_KAIJU { def container_image = "kaiju:1.8.2--h5b5514e_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path(db) diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf index 2c848ecff07..62b8e48dd4f 100644 --- a/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -6,7 +6,6 @@ process KAIJU_KAIJU2KRONA { def container_image = "kaiju:1.8.2--h5b5514e_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(tsv) path(db) diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf index 31c7cc312db..a0e131ca86e 100644 --- a/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/modules/nf-core/kaiju/kaiju2table/main.nf @@ -6,7 +6,6 @@ process KAIJU_KAIJU2TABLE { def container_image = "kaiju:1.8.2--h5b5514e_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(results) path db diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index 3c212697fea..df8bd75ef72 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -6,7 +6,6 @@ process KALLISTO_INDEX { def container_image = "kallisto:0.46.2--h4f7b962_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index 2282dd275c2..35989f390a2 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -6,7 +6,6 @@ process KALLISTOBUSTOOLS_COUNT { def container_image = "kb-python:0.27.2--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index e747d524b2a..c791329a5ff 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -6,7 +6,6 @@ process KALLISTOBUSTOOLS_REF { def container_image = "kb-python:0.27.2--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path gtf diff --git a/modules/nf-core/kat/hist/main.nf b/modules/nf-core/kat/hist/main.nf index 1fd3e6e568b..d883b6a7ab4 100644 --- a/modules/nf-core/kat/hist/main.nf +++ b/modules/nf-core/kat/hist/main.nf @@ -6,7 +6,6 @@ process KAT_HIST { def container_image = "kat:2.4.2--py38hfc5f9d8_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/khmer/normalizebymedian/main.nf b/modules/nf-core/khmer/normalizebymedian/main.nf index 5f0722f5a90..77f54dca8e2 100644 --- a/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/modules/nf-core/khmer/normalizebymedian/main.nf @@ -6,7 +6,6 @@ process KHMER_NORMALIZEBYMEDIAN { def container_image = "khmer:3.0.0a3--py37haa7609a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path pe_reads path se_reads diff --git a/modules/nf-core/khmer/uniquekmers/main.nf b/modules/nf-core/khmer/uniquekmers/main.nf index ecd6e7af44e..8680cab5deb 100644 --- a/modules/nf-core/khmer/uniquekmers/main.nf +++ b/modules/nf-core/khmer/uniquekmers/main.nf @@ -6,7 +6,6 @@ process KHMER_UNIQUEKMERS { def container_image = "khmer:3.0.0a3--py37haa7609a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta val kmer_size diff --git a/modules/nf-core/kleborate/main.nf b/modules/nf-core/kleborate/main.nf index 3253fec40ab..b361e7f2601 100644 --- a/modules/nf-core/kleborate/main.nf +++ b/modules/nf-core/kleborate/main.nf @@ -6,7 +6,6 @@ process KLEBORATE { def container_image = "kleborate:2.1.0--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastas) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 2d3f2788c53..04c1a7d2efd 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -6,7 +6,6 @@ process KRAKEN2_KRAKEN2 { def container_image = "mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path db diff --git a/modules/nf-core/krakentools/combinekreports/main.nf b/modules/nf-core/krakentools/combinekreports/main.nf index dbade9d9284..cc40484c7ec 100644 --- a/modules/nf-core/krakentools/combinekreports/main.nf +++ b/modules/nf-core/krakentools/combinekreports/main.nf @@ -5,7 +5,6 @@ process KRAKENTOOLS_COMBINEKREPORTS { def container_image = "krakentools:1.2--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(kreports) diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf index 09bdf078d42..f5ca26fa3bf 100644 --- a/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/modules/nf-core/krakentools/kreport2krona/main.nf @@ -7,7 +7,6 @@ process KRAKENTOOLS_KREPORT2KRONA { def container_image = "krakentools:1.2--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(kreport) diff --git a/modules/nf-core/krona/kronadb/main.nf b/modules/nf-core/krona/kronadb/main.nf index 6ec1109d451..13952eb4869 100644 --- a/modules/nf-core/krona/kronadb/main.nf +++ b/modules/nf-core/krona/kronadb/main.nf @@ -7,7 +7,6 @@ process KRONA_KRONADB { def container_image = "krona:2.7.1--pl526_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - output: path 'taxonomy/taxonomy.tab', emit: db path "versions.yml" , emit: versions diff --git a/modules/nf-core/krona/ktimporttaxonomy/main.nf b/modules/nf-core/krona/ktimporttaxonomy/main.nf index d70f820b253..3b4cc89328e 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -7,7 +7,6 @@ process KRONA_KTIMPORTTAXONOMY { def container_image = "krona:2.8--pl5262hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) path taxonomy, stageAs: 'taxonomy.tab' diff --git a/modules/nf-core/krona/ktimporttext/main.nf b/modules/nf-core/krona/ktimporttext/main.nf index 64df1f0d179..97aa4fd7a39 100644 --- a/modules/nf-core/krona/ktimporttext/main.nf +++ b/modules/nf-core/krona/ktimporttext/main.nf @@ -6,7 +6,6 @@ process KRONA_KTIMPORTTEXT { def container_image = "krona:2.8.1--pl5321hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(report) diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index 6cb60e15341..fa740598a43 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -7,7 +7,6 @@ process KRONA_KTUPDATETAXONOMY { def container_image = "krona:2.7.1--pl526_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - output: path 'taxonomy/taxonomy.tab', emit: db path "versions.yml" , emit: versions diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 03487a97839..85c3f878045 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -6,7 +6,6 @@ process LAST_DOTPLOT { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(maf) val(format) diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 7ffe727edf1..158c045f153 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -6,7 +6,6 @@ process LAST_LASTAL { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastx), path (param_file) path index diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 925da314c9f..6c8e8bea423 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -6,7 +6,6 @@ process LAST_LASTDB { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index b6332f939a5..0a12cefc96b 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -6,7 +6,6 @@ process LAST_MAFCONVERT { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(maf) val(format) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 0c752b103d3..6c6f86e9ab0 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -6,7 +6,6 @@ process LAST_MAFSWAP { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index 54a7b571c70..d2e5f40e5e9 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -6,7 +6,6 @@ process LAST_POSTMASK { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index f32b1e3a0de..6f855f41f55 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -6,7 +6,6 @@ process LAST_SPLIT { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index da8aff592e0..1cfdc0837d2 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -6,7 +6,6 @@ process LAST_TRAIN { def container_image = "last:1250--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastx) path index diff --git a/modules/nf-core/leehom/main.nf b/modules/nf-core/leehom/main.nf index 24731286406..1222757a498 100644 --- a/modules/nf-core/leehom/main.nf +++ b/modules/nf-core/leehom/main.nf @@ -7,7 +7,6 @@ process LEEHOM { def container_image = "leehom:1.2.15--h29e30f7_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index a7cd15bf781..e8d00b774b1 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -6,7 +6,6 @@ process LEGSTA { def container_image = "legsta:0.5.1--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 8b22222965a..fa179305b7b 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -6,7 +6,6 @@ process LIMA { def container_image = "lima:2.2.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ccs) path primers diff --git a/modules/nf-core/lissero/main.nf b/modules/nf-core/lissero/main.nf index f72b8ab3e8e..af6337eadbd 100644 --- a/modules/nf-core/lissero/main.nf +++ b/modules/nf-core/lissero/main.nf @@ -6,7 +6,6 @@ process LISSERO { def container_image = "lissero:0.4.9--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/lofreq/call/main.nf b/modules/nf-core/lofreq/call/main.nf index a4ccf9e07ad..e1cfbe2da8c 100644 --- a/modules/nf-core/lofreq/call/main.nf +++ b/modules/nf-core/lofreq/call/main.nf @@ -6,7 +6,6 @@ process LOFREQ_CALL { def container_image = "lofreq:2.1.5--py38h588ecb2_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf index 2f0e98078a8..b2306f77d26 100644 --- a/modules/nf-core/lofreq/callparallel/main.nf +++ b/modules/nf-core/lofreq/callparallel/main.nf @@ -6,7 +6,6 @@ process LOFREQ_CALLPARALLEL { def container_image = "lofreq:2.1.5--py38h588ecb2_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path fasta diff --git a/modules/nf-core/lofreq/filter/main.nf b/modules/nf-core/lofreq/filter/main.nf index 5f28a1fb2df..649911e9680 100644 --- a/modules/nf-core/lofreq/filter/main.nf +++ b/modules/nf-core/lofreq/filter/main.nf @@ -6,7 +6,6 @@ process LOFREQ_FILTER { def container_image = "lofreq:2.1.5--py38h588ecb2_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/lofreq/indelqual/main.nf b/modules/nf-core/lofreq/indelqual/main.nf index b6562df1365..fd8287d14c2 100644 --- a/modules/nf-core/lofreq/indelqual/main.nf +++ b/modules/nf-core/lofreq/indelqual/main.nf @@ -6,7 +6,6 @@ process LOFREQ_INDELQUAL { def container_image = "lofreq:2.1.5--py38h588ecb2_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/macrel/contigs/main.nf b/modules/nf-core/macrel/contigs/main.nf index fd79613682a..0fae818d4b0 100644 --- a/modules/nf-core/macrel/contigs/main.nf +++ b/modules/nf-core/macrel/contigs/main.nf @@ -6,7 +6,6 @@ process MACREL_CONTIGS { def container_image = "macrel:1.1.0--py36hc5360cc_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf index 4b4e7fefd19..162a8641d99 100644 --- a/modules/nf-core/macs2/callpeak/main.nf +++ b/modules/nf-core/macs2/callpeak/main.nf @@ -6,7 +6,6 @@ process MACS2_CALLPEAK { def container_image = "macs2:2.2.7.1--py38h4a8c8d9_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ipbam), path(controlbam) val macs2_gsize diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 7215ff4d211..5193fe4caf9 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -6,7 +6,6 @@ process MAFFT { def container_image = "mafft:7.490--h779adbc_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 74ab149f18f..3628e559a6a 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -6,7 +6,6 @@ process MALT_BUILD { def container_image = "malt:0.41--1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fastas val seq_type diff --git a/modules/nf-core/malt/run/main.nf b/modules/nf-core/malt/run/main.nf index 6e687e70f05..eb296b65c53 100644 --- a/modules/nf-core/malt/run/main.nf +++ b/modules/nf-core/malt/run/main.nf @@ -6,7 +6,6 @@ process MALT_RUN { def container_image = "malt:0.41--1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastqs) val mode diff --git a/modules/nf-core/maltextract/main.nf b/modules/nf-core/maltextract/main.nf index 6e3df6b4ac9..8913b976d6e 100644 --- a/modules/nf-core/maltextract/main.nf +++ b/modules/nf-core/maltextract/main.nf @@ -6,7 +6,6 @@ process MALTEXTRACT { def container_image = "hops:0.35--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path rma6 path taxon_list diff --git a/modules/nf-core/manta/convertinversion/main.nf b/modules/nf-core/manta/convertinversion/main.nf index e4b7ce5e9cc..829128af4db 100644 --- a/modules/nf-core/manta/convertinversion/main.nf +++ b/modules/nf-core/manta/convertinversion/main.nf @@ -6,7 +6,6 @@ process MANTA_CONVERTINVERSION { def container_image = "mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) path fasta diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index 2b95619c986..bb35141d31f 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -6,7 +6,6 @@ process MANTA_GERMLINE { def container_image = "manta:1.6.0--h9ee0642_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi) diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf index d68e7690d2a..082d355086e 100644 --- a/modules/nf-core/manta/somatic/main.nf +++ b/modules/nf-core/manta/somatic/main.nf @@ -6,7 +6,6 @@ process MANTA_SOMATIC { def container_image = "manta:1.6.0--h9ee0642_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi) path fasta diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf index 5357f1bf8ef..d08019a4e52 100644 --- a/modules/nf-core/manta/tumoronly/main.nf +++ b/modules/nf-core/manta/tumoronly/main.nf @@ -6,7 +6,6 @@ process MANTA_TUMORONLY { def container_image = "manta:1.6.0--h9ee0642_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi) path fasta diff --git a/modules/nf-core/mapdamage2/main.nf b/modules/nf-core/mapdamage2/main.nf index a462358ab6f..fffb7536d6c 100644 --- a/modules/nf-core/mapdamage2/main.nf +++ b/modules/nf-core/mapdamage2/main.nf @@ -6,7 +6,6 @@ process MAPDAMAGE2 { def container_image = "mapdamage2:2.2.1--pyr40_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path(fasta) diff --git a/modules/nf-core/mash/dist/main.nf b/modules/nf-core/mash/dist/main.nf index a4a48f159aa..46820385408 100644 --- a/modules/nf-core/mash/dist/main.nf +++ b/modules/nf-core/mash/dist/main.nf @@ -6,7 +6,6 @@ process MASH_DIST { def container_image = "mash:2.3--he348c14_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(query) path reference diff --git a/modules/nf-core/mash/screen/main.nf b/modules/nf-core/mash/screen/main.nf index ddee9832330..bea21391841 100644 --- a/modules/nf-core/mash/screen/main.nf +++ b/modules/nf-core/mash/screen/main.nf @@ -6,7 +6,6 @@ process MASH_SCREEN { def container_image = "mash:2.3--he348c14_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(query) path sequences_sketch diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf index d0a57e4aa92..2434c184315 100644 --- a/modules/nf-core/mash/sketch/main.nf +++ b/modules/nf-core/mash/sketch/main.nf @@ -5,7 +5,6 @@ process MASH_SKETCH { def container_image = "mash:2.3--he348c14_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mashtree/main.nf b/modules/nf-core/mashtree/main.nf index 79c7c3ea797..ab0a55f6ab0 100644 --- a/modules/nf-core/mashtree/main.nf +++ b/modules/nf-core/mashtree/main.nf @@ -6,7 +6,6 @@ process MASHTREE { def container_image = "mashtree:1.2.0--pl526h516909a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 03e0535ff4f..364d2f8bbc2 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -6,7 +6,6 @@ process MAXBIN2 { def container_image = "maxbin2:2.2.7--he1b5a44_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(contigs), path(reads), path(abund) diff --git a/modules/nf-core/maxquant/lfq/main.nf b/modules/nf-core/maxquant/lfq/main.nf index b888d36b6bf..9ee83e5ed37 100644 --- a/modules/nf-core/maxquant/lfq/main.nf +++ b/modules/nf-core/maxquant/lfq/main.nf @@ -6,7 +6,6 @@ process MAXQUANT_LFQ { def container_image = "maxquant:2.0.3.0--py310hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta), path(paramfile) path raw diff --git a/modules/nf-core/mcroni/main.nf b/modules/nf-core/mcroni/main.nf index 0ec3a103a6c..eeb3e124b9c 100644 --- a/modules/nf-core/mcroni/main.nf +++ b/modules/nf-core/mcroni/main.nf @@ -7,7 +7,6 @@ process MCRONI { def container_image = "mcroni:1.0.4--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index 4df7bbe5d2b..ecb9c11e648 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -6,7 +6,6 @@ process MD5SUM { def container_image = "ubuntu:20.04" container [ params.container_registry ?: '' , container_image ].join('/') - input: tuple val(meta), path(file) diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf index dbbefd65bad..ed318d0b44b 100644 --- a/modules/nf-core/medaka/main.nf +++ b/modules/nf-core/medaka/main.nf @@ -6,7 +6,6 @@ process MEDAKA { def container_image = "medaka:1.4.4--py38h130def0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), path(assembly) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 2e5f03d5986..116453a3afe 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -6,7 +6,6 @@ process MEGAHIT { def container_image = "mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/megan/daa2info/main.nf b/modules/nf-core/megan/daa2info/main.nf index 6fef5a26d30..4e606b722ca 100644 --- a/modules/nf-core/megan/daa2info/main.nf +++ b/modules/nf-core/megan/daa2info/main.nf @@ -6,7 +6,6 @@ process MEGAN_DAA2INFO { def container_image = "megan:6.21.7--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(daa) val(megan_summary) diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index 66b9ae81544..201e0462284 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -6,7 +6,6 @@ process MEGAN_RMA2INFO { def container_image = "megan:6.21.7--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(rma6) val(megan_summary) diff --git a/modules/nf-core/meningotype/main.nf b/modules/nf-core/meningotype/main.nf index 2f3cb3f3825..dfe5e81da13 100644 --- a/modules/nf-core/meningotype/main.nf +++ b/modules/nf-core/meningotype/main.nf @@ -6,7 +6,6 @@ process MENINGOTYPE { def container_image = "meningotype:0.8.5--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/merqury/main.nf b/modules/nf-core/merqury/main.nf index 89bd6d3e6fe..843d76a8211 100644 --- a/modules/nf-core/merqury/main.nf +++ b/modules/nf-core/merqury/main.nf @@ -6,7 +6,6 @@ process MERQURY { def container_image = "merqury:1.3--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(meryl_db), path(assembly) diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index c24f8e26c9d..f518e0873f3 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -6,7 +6,6 @@ process MERYL_COUNT { def container_image = "meryl:1.3--h87f3376_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 11a717bd140..373122c9e7b 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -6,7 +6,6 @@ process MERYL_HISTOGRAM { def container_image = "meryl:1.3--h87f3376_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(meryl_db) diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index d10255a1478..86ded63e523 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -6,7 +6,6 @@ process MERYL_UNIONSUM { def container_image = "meryl:1.3--h87f3376_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(meryl_dbs) diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 2bd8c8b253d..62f584df359 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -6,7 +6,6 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { def container_image = "metabat2:2.15--h986a166_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf index 0af0fe49d5b..c33568c7e11 100644 --- a/modules/nf-core/metabat2/metabat2/main.nf +++ b/modules/nf-core/metabat2/metabat2/main.nf @@ -6,7 +6,6 @@ process METABAT2_METABAT2 { def container_image = "metabat2:2.15--h986a166_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta), path(depth) diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index e957c150ba1..841e663327a 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -5,7 +5,6 @@ process METAPHLAN3_MERGEMETAPHLANTABLES { def container_image = "metaphlan:3.0.12--pyhb7b1952_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(profiles) diff --git a/modules/nf-core/metaphlan3/metaphlan3/main.nf b/modules/nf-core/metaphlan3/metaphlan3/main.nf index b42f8b39fa2..0a423380fa4 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -6,7 +6,6 @@ process METAPHLAN3_METAPHLAN3 { def container_image = "metaphlan:3.0.12--pyhb7b1952_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) path metaphlan_db diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 91e8a9d20c5..32e5961f88d 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -6,7 +6,6 @@ process METHYLDACKEL_EXTRACT { def container_image = "methyldackel:0.6.0--h22771d5_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path fasta diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index ed696aa08e5..4786b84699d 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -6,7 +6,6 @@ process METHYLDACKEL_MBIAS { def container_image = "methyldackel:0.6.0--h22771d5_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path fasta diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index ee85602992e..03e899af696 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -6,7 +6,6 @@ process MINIA { def container_image = "minia:3.2.6--h9a82719_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index 61b9cdff5d5..eb6697cd2b5 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -6,7 +6,6 @@ process MINIASM { def container_image = "miniasm:0.3_r179--h5bf99c6_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), path(paf) diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index c776418349c..147ba71ce07 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -6,7 +6,6 @@ process MINIMAP2_ALIGN { def container_image = "mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path reference @@ -39,7 +38,6 @@ process MINIMAP2_ALIGN { $set_cigar_bam \\ $bam_output - cat <<-END_VERSIONS > versions.yml "${task.process}": minimap2: \$(minimap2 --version 2>&1) diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf index 508cb37877f..972109c9f92 100644 --- a/modules/nf-core/minimap2/index/main.nf +++ b/modules/nf-core/minimap2/index/main.nf @@ -5,7 +5,6 @@ process MINIMAP2_INDEX { def container_image = "minimap2:2.21--h5bf99c6_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 7f20592503e..594aa712910 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -6,7 +6,6 @@ process MLST { def container_image = "mlst:2.19.0--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mobsuite/recon/main.nf b/modules/nf-core/mobsuite/recon/main.nf index 844e5d3d292..93cd91b4dd2 100644 --- a/modules/nf-core/mobsuite/recon/main.nf +++ b/modules/nf-core/mobsuite/recon/main.nf @@ -6,7 +6,6 @@ process MOBSUITE_RECON { def container_image = "mob_suite:3.0.3--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 32e8478630d..9e3c88a3129 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -6,7 +6,6 @@ process MOSDEPTH { def container_image = "mosdepth:0.3.3--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path bed diff --git a/modules/nf-core/motus/downloaddb/main.nf b/modules/nf-core/motus/downloaddb/main.nf index 1ecc14be703..5f5f8c4049a 100644 --- a/modules/nf-core/motus/downloaddb/main.nf +++ b/modules/nf-core/motus/downloaddb/main.nf @@ -5,7 +5,6 @@ process MOTUS_DOWNLOADDB { def container_image = "motus:3.0.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path motus_downloaddb_script diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 5d8f7911542..95b842ea1b8 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -8,7 +8,6 @@ process MOTUS_MERGE { def container_image = "motus:3.0.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf index c9e02852ba6..8728b6fa220 100644 --- a/modules/nf-core/motus/profile/main.nf +++ b/modules/nf-core/motus/profile/main.nf @@ -6,7 +6,6 @@ process MOTUS_PROFILE { def container_image = "motus:3.0.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path db diff --git a/modules/nf-core/msisensor/msi/main.nf b/modules/nf-core/msisensor/msi/main.nf index 0c4964aed62..ff66f2215a3 100644 --- a/modules/nf-core/msisensor/msi/main.nf +++ b/modules/nf-core/msisensor/msi/main.nf @@ -6,7 +6,6 @@ process MSISENSOR_MSI { def container_image = "msisensor:0.5--hb3646a4_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers) diff --git a/modules/nf-core/msisensor/scan/main.nf b/modules/nf-core/msisensor/scan/main.nf index 3c996075cf7..e1c204d409c 100644 --- a/modules/nf-core/msisensor/scan/main.nf +++ b/modules/nf-core/msisensor/scan/main.nf @@ -6,7 +6,6 @@ process MSISENSOR_SCAN { def container_image = "msisensor:0.5--hb3646a4_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf index 355cf3f43ae..099abedfa64 100644 --- a/modules/nf-core/msisensor2/msi/main.nf +++ b/modules/nf-core/msisensor2/msi/main.nf @@ -6,7 +6,6 @@ process MSISENSOR2_MSI { def container_image = "msisensor2:0.1--hd03093a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) path scan diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf index c91e35ee1aa..012e1ad9b6e 100644 --- a/modules/nf-core/msisensor2/scan/main.nf +++ b/modules/nf-core/msisensor2/scan/main.nf @@ -6,7 +6,6 @@ process MSISENSOR2_SCAN { def container_image = "msisensor2:0.1--hd03093a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta val output diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf index 45dbf2dc90b..5f774ad2fe8 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -6,7 +6,6 @@ process MSISENSORPRO_MSI_SOMATIC { def container_image = "msisensor-pro:1.2.0--hfc31af2_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) path (fasta) diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf index a6cd3dde079..5f77c4c3350 100644 --- a/modules/nf-core/msisensorpro/scan/main.nf +++ b/modules/nf-core/msisensorpro/scan/main.nf @@ -6,7 +6,6 @@ process MSISENSORPRO_SCAN { def container_image = "msisensor-pro:1.2.0--hfc31af2_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mtnucratio/main.nf b/modules/nf-core/mtnucratio/main.nf index c71f21da3f4..e1ac6f425a4 100644 --- a/modules/nf-core/mtnucratio/main.nf +++ b/modules/nf-core/mtnucratio/main.nf @@ -6,7 +6,6 @@ process MTNUCRATIO { def container_image = "mtnucratio:0.7--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) val(mt_id) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 0a0d618c196..bf5c6173ebe 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -5,7 +5,6 @@ process MULTIQC { def container_image = "multiqc:1.13--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path multiqc_files, stageAs: "?/*" path(multiqc_config) diff --git a/modules/nf-core/multivcfanalyzer/main.nf b/modules/nf-core/multivcfanalyzer/main.nf index 74aa3fd9059..f86aa89d88d 100644 --- a/modules/nf-core/multivcfanalyzer/main.nf +++ b/modules/nf-core/multivcfanalyzer/main.nf @@ -6,7 +6,6 @@ process MULTIVCFANALYZER { def container_image = "multivcfanalyzer:0.85.2--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path vcfs path fasta @@ -19,7 +18,6 @@ process MULTIVCFANALYZER { val heterozygous_freq path gff_exclude - output: path('fullAlignment.fasta.gz') , emit: full_alignment path('info.txt') , emit: info_txt diff --git a/modules/nf-core/mummer/main.nf b/modules/nf-core/mummer/main.nf index 9928e269656..53ee2d8a92c 100644 --- a/modules/nf-core/mummer/main.nf +++ b/modules/nf-core/mummer/main.nf @@ -7,7 +7,6 @@ process MUMMER { def container_image = "mummer:3.23--pl5262h1b792b2_12" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf index 0e51ab58ef2..740f4738b43 100644 --- a/modules/nf-core/muscle/main.nf +++ b/modules/nf-core/muscle/main.nf @@ -6,7 +6,6 @@ process MUSCLE { def container_image = "muscle:3.8.1551--h7d875b9_6" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mykrobe/predict/main.nf b/modules/nf-core/mykrobe/predict/main.nf index f15177b8577..d3b2d9a3ec4 100644 --- a/modules/nf-core/mykrobe/predict/main.nf +++ b/modules/nf-core/mykrobe/predict/main.nf @@ -6,7 +6,6 @@ process MYKROBE_PREDICT { def container_image = "mykrobe:0.11.0--py39h2add14b_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(seqs) val species diff --git a/modules/nf-core/nanolyse/main.nf b/modules/nf-core/nanolyse/main.nf index ccc17c52ff8..99e65f30d8b 100644 --- a/modules/nf-core/nanolyse/main.nf +++ b/modules/nf-core/nanolyse/main.nf @@ -6,7 +6,6 @@ process NANOLYSE { def container_image = "nanolyse:1.2.0--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq) path fasta diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index 4c7356547f5..783d43035aa 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -6,7 +6,6 @@ process NANOPLOT { def container_image = "nanoplot:1.40.0--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/ncbigenomedownload/main.nf b/modules/nf-core/ncbigenomedownload/main.nf index e3819ab2ab1..647bd9f5b9c 100644 --- a/modules/nf-core/ncbigenomedownload/main.nf +++ b/modules/nf-core/ncbigenomedownload/main.nf @@ -6,7 +6,6 @@ process NCBIGENOMEDOWNLOAD { def container_image = "ncbi-genome-download:0.3.1--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: val meta path accessions diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 22e89d55591..c4dfe7ab588 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -6,7 +6,6 @@ process NEXTCLADE_DATASETGET { def container_image = "nextclade:2.2.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: val dataset val reference diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 70e06df09e6..62b58520647 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -6,7 +6,6 @@ process NEXTCLADE_RUN { def container_image = "nextclade:2.2.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path dataset diff --git a/modules/nf-core/nextgenmap/main.nf b/modules/nf-core/nextgenmap/main.nf index c3ba5174675..22470b29630 100644 --- a/modules/nf-core/nextgenmap/main.nf +++ b/modules/nf-core/nextgenmap/main.nf @@ -6,7 +6,6 @@ process NEXTGENMAP { def container_image = "nextgenmap:0.5.5--hc9558a2_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path(fasta) diff --git a/modules/nf-core/ngmaster/main.nf b/modules/nf-core/ngmaster/main.nf index 602acaaa5fe..f80385cacc6 100644 --- a/modules/nf-core/ngmaster/main.nf +++ b/modules/nf-core/ngmaster/main.nf @@ -6,7 +6,6 @@ process NGMASTER { def container_image = "ngmaster:0.5.8--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf index 92fe2e82811..c57442b30c7 100644 --- a/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/modules/nf-core/ngscheckmate/ncm/main.nf @@ -5,7 +5,6 @@ process NGSCHECKMATE_NCM { def container_image = "ngscheckmate:1.0.0--py27r41hdfd78af_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path files path snp_bed diff --git a/modules/nf-core/nucmer/main.nf b/modules/nf-core/nucmer/main.nf index d58b778bb7f..c510c2016d7 100644 --- a/modules/nf-core/nucmer/main.nf +++ b/modules/nf-core/nucmer/main.nf @@ -6,7 +6,6 @@ process NUCMER { def container_image = "mummer:3.23--pl5262h1b792b2_12" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ref), path(query) diff --git a/modules/nf-core/optitype/main.nf b/modules/nf-core/optitype/main.nf index 0a9c1f6d01e..c1b5250703b 100644 --- a/modules/nf-core/optitype/main.nf +++ b/modules/nf-core/optitype/main.nf @@ -6,7 +6,6 @@ process OPTITYPE { def container_image = "optitype:1.3.5--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pairix/main.nf b/modules/nf-core/pairix/main.nf index fed85537015..844c5c1fcf4 100644 --- a/modules/nf-core/pairix/main.nf +++ b/modules/nf-core/pairix/main.nf @@ -6,7 +6,6 @@ process PAIRIX { def container_image = "pairix:0.3.7--py36h30a8e3e_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pair) diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf index 8c3022cf059..bf8618a9557 100644 --- a/modules/nf-core/pairtools/dedup/main.nf +++ b/modules/nf-core/pairtools/dedup/main.nf @@ -6,7 +6,6 @@ process PAIRTOOLS_DEDUP { def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf index 9054298c8cb..f5b90c6bd7e 100644 --- a/modules/nf-core/pairtools/flip/main.nf +++ b/modules/nf-core/pairtools/flip/main.nf @@ -6,7 +6,6 @@ process PAIRTOOLS_FLIP { def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(sam) path chromsizes diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf index 46b9e4a0f2b..ca3f1a71e68 100644 --- a/modules/nf-core/pairtools/parse/main.nf +++ b/modules/nf-core/pairtools/parse/main.nf @@ -6,7 +6,6 @@ process PAIRTOOLS_PARSE { def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path chromsizes diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf index 9540d3fff50..b041c108b8f 100644 --- a/modules/nf-core/pairtools/restrict/main.nf +++ b/modules/nf-core/pairtools/restrict/main.nf @@ -6,7 +6,6 @@ process PAIRTOOLS_RESTRICT { def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pairs) path frag diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf index 7a2f82c2125..ac44ede7555 100644 --- a/modules/nf-core/pairtools/select/main.nf +++ b/modules/nf-core/pairtools/select/main.nf @@ -6,7 +6,6 @@ process PAIRTOOLS_SELECT { def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf index e72449056b0..f6dbf1c8a81 100644 --- a/modules/nf-core/pairtools/sort/main.nf +++ b/modules/nf-core/pairtools/sort/main.nf @@ -6,7 +6,6 @@ process PAIRTOOLS_SORT { def container_image = "pairtools:0.3.0--py37hb9c2fc3_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/panaroo/run/main.nf b/modules/nf-core/panaroo/run/main.nf index a85e7bb16c5..15385400cd2 100644 --- a/modules/nf-core/panaroo/run/main.nf +++ b/modules/nf-core/panaroo/run/main.nf @@ -6,7 +6,6 @@ process PANAROO_RUN { def container_image = "panaroo:1.2.9--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gff) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 6ec4ce64f9c..ad90ad32f1e 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -6,7 +6,6 @@ process PANGOLIN { def container_image = "pangolin:4.1.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/paraclu/main.nf b/modules/nf-core/paraclu/main.nf index 52bc42d47b0..1583ea49b14 100644 --- a/modules/nf-core/paraclu/main.nf +++ b/modules/nf-core/paraclu/main.nf @@ -7,7 +7,6 @@ process PARACLU { def container_image = "paraclu:10--h9a82719_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) val(min_cluster) diff --git a/modules/nf-core/pasty/main.nf b/modules/nf-core/pasty/main.nf index 445c022bd71..043febcb8dc 100644 --- a/modules/nf-core/pasty/main.nf +++ b/modules/nf-core/pasty/main.nf @@ -6,7 +6,6 @@ process PASTY { def container_image = "pasty:1.0.0--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pbbam/pbmerge/main.nf b/modules/nf-core/pbbam/pbmerge/main.nf index 98d6d02c4b1..05fddde440d 100644 --- a/modules/nf-core/pbbam/pbmerge/main.nf +++ b/modules/nf-core/pbbam/pbmerge/main.nf @@ -6,7 +6,6 @@ process PBBAM_PBMERGE { def container_image = "pbbam:1.7.0--h058f120_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 1dc2f20cae4..e35ceedf675 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -6,7 +6,6 @@ process PBCCS { def container_image = "pbccs:6.2.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(pbi) val chunk_num diff --git a/modules/nf-core/pbptyper/main.nf b/modules/nf-core/pbptyper/main.nf index 05896d2afbe..7a7892696b2 100644 --- a/modules/nf-core/pbptyper/main.nf +++ b/modules/nf-core/pbptyper/main.nf @@ -6,7 +6,6 @@ process PBPTYPER { def container_image = "pbptyper:1.0.2--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path(db) diff --git a/modules/nf-core/pear/main.nf b/modules/nf-core/pear/main.nf index 7c1666f2b8a..8fc6e158dc7 100644 --- a/modules/nf-core/pear/main.nf +++ b/modules/nf-core/pear/main.nf @@ -6,7 +6,6 @@ process PEAR { def container_image = "pear:0.9.6--h67092d7_8" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index dca940a4e14..80feb459013 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -6,7 +6,6 @@ process PEDDY { def container_image = "peddy:0.4.8--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(vcf_tbi) path ped diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index 11cd707a68c..f65263fd86c 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -7,7 +7,6 @@ process PHANTOMPEAKQUALTOOLS { def container_image = "phantompeakqualtools:1.2.2--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf index c1a520e80d9..ab4be1a7d4b 100644 --- a/modules/nf-core/phyloflash/main.nf +++ b/modules/nf-core/phyloflash/main.nf @@ -6,7 +6,6 @@ process PHYLOFLASH { def container_image = "phyloflash:3.4--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path silva_db diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 60e514a2d6a..ca5511e19b3 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -6,7 +6,6 @@ process PICARD_ADDORREPLACEREADGROUPS { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 10626eef9eb..080e710bc2c 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -6,7 +6,6 @@ process PICARD_CLEANSAM { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index d9d92b235f9..503c64338ca 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -6,7 +6,6 @@ process PICARD_COLLECTHSMETRICS { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta @@ -43,7 +42,6 @@ process PICARD_COLLECTHSMETRICS { --INPUT $bam \\ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics - cat <<-END_VERSIONS > versions.yml "${task.process}": picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 4ff2098c587..5f8fcfa3c17 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -6,7 +6,6 @@ process PICARD_COLLECTMULTIPLEMETRICS { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index e2a46ebe263..670c69222df 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -6,7 +6,6 @@ process PICARD_COLLECTWGSMETRICS { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta @@ -36,7 +35,6 @@ process PICARD_COLLECTWGSMETRICS { --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ --REFERENCE_SEQUENCE ${fasta} - cat <<-END_VERSIONS > versions.yml "${task.process}": picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 87efe40f8a0..1772e31a2d5 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -6,7 +6,6 @@ process PICARD_CREATESEQUENCEDICTIONARY { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index bb3d94a9a94..62e8d1839f4 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -6,7 +6,6 @@ process PICARD_CROSSCHECKFINGERPRINTS { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input1) path input2 diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index 46be4ee0954..2bad3537c4d 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -6,7 +6,6 @@ process PICARD_FASTQTOSAM { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index a446dcbbfdd..1dc24d7aedb 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -6,7 +6,6 @@ process PICARD_FILTERSAMREADS { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(readlist) val filter diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index 9080f74fe68..0333f3ee5e0 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -6,7 +6,6 @@ process PICARD_FIXMATEINFORMATION { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 51189ba1954..8f835f0da6c 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -6,7 +6,6 @@ process PICARD_LIFTOVERVCF { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_vcf) path dict diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 493f4b13375..c54d5f9b6c2 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -6,7 +6,6 @@ process PICARD_MARKDUPLICATES { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path fasta diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 3e3b6120a09..cf95fc6c2f3 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -6,7 +6,6 @@ process PICARD_MERGESAMFILES { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 782ac3dbd7a..040933e7977 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -7,7 +7,6 @@ process PICARD_RENAMESAMPLEINVCF { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index b9765c26ace..981be8ade89 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -6,7 +6,6 @@ process PICARD_SORTSAM { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) val sort_order diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 463f9d24cbc..3829f791891 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -6,7 +6,6 @@ process PICARD_SORTVCF { def container_image = "picard:2.27.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) path reference diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index 70d04cf42a5..6e6f64486cb 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -6,7 +6,6 @@ process PINTS_CALLER { def container_image = "pypints:1.1.6--pyh5e36f6f_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bams) diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf index c32dae56270..41797adace1 100644 --- a/modules/nf-core/pirate/main.nf +++ b/modules/nf-core/pirate/main.nf @@ -6,7 +6,6 @@ process PIRATE { def container_image = "pirate:1.0.4--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gff) diff --git a/modules/nf-core/plasmidfinder/main.nf b/modules/nf-core/plasmidfinder/main.nf index 4436fe30bd8..7dadca4abd3 100644 --- a/modules/nf-core/plasmidfinder/main.nf +++ b/modules/nf-core/plasmidfinder/main.nf @@ -7,7 +7,6 @@ process PLASMIDFINDER { def container_image = "plasmidfinder:2.1.6--py310hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index c85d57c2fef..6fc4544158b 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -6,7 +6,6 @@ process PLASMIDID { def container_image = "plasmidid:1.6.5--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(scaffold) path fasta diff --git a/modules/nf-core/plink/extract/main.nf b/modules/nf-core/plink/extract/main.nf index 5ba39535625..55e1c93b043 100644 --- a/modules/nf-core/plink/extract/main.nf +++ b/modules/nf-core/plink/extract/main.nf @@ -6,7 +6,6 @@ process PLINK_EXTRACT { def container_image = "plink:1.90b6.21--h779adbc_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) diff --git a/modules/nf-core/plink/vcf/main.nf b/modules/nf-core/plink/vcf/main.nf index a8d80a7ff2f..033b771065f 100644 --- a/modules/nf-core/plink/vcf/main.nf +++ b/modules/nf-core/plink/vcf/main.nf @@ -6,7 +6,6 @@ process PLINK_VCF { def container_image = "plink:1.90b6.21--h779adbc_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/plink2/extract/main.nf b/modules/nf-core/plink2/extract/main.nf index 60d2e53502e..0fa6c564f13 100644 --- a/modules/nf-core/plink2/extract/main.nf +++ b/modules/nf-core/plink2/extract/main.nf @@ -6,7 +6,6 @@ process PLINK2_EXTRACT { def container_image = "plink2:2.00a2.3--h712d239_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pgen), path(psam), path(pvar), path(variants) diff --git a/modules/nf-core/plink2/score/main.nf b/modules/nf-core/plink2/score/main.nf index be2a2dc30d7..70fd9f713fd 100644 --- a/modules/nf-core/plink2/score/main.nf +++ b/modules/nf-core/plink2/score/main.nf @@ -6,7 +6,6 @@ process PLINK2_SCORE { def container_image = "plink2:2.00a2.3--h712d239_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(pgen), path(psam), path(pvar) path(scorefile) diff --git a/modules/nf-core/plink2/vcf/main.nf b/modules/nf-core/plink2/vcf/main.nf index f9bd89729f0..4ac8a15b1da 100644 --- a/modules/nf-core/plink2/vcf/main.nf +++ b/modules/nf-core/plink2/vcf/main.nf @@ -6,7 +6,6 @@ process PLINK2_VCF { def container_image = "plink2:2.00a2.3--h712d239_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf index a685e7bf257..9715a847d1b 100644 --- a/modules/nf-core/pmdtools/filter/main.nf +++ b/modules/nf-core/pmdtools/filter/main.nf @@ -6,7 +6,6 @@ process PMDTOOLS_FILTER { def container_image = "pmdtools:0.60--hdfd78af_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path (bai) val(threshold) diff --git a/modules/nf-core/porechop/main.nf b/modules/nf-core/porechop/main.nf index e911e2d7d33..7f8ddd481f4 100644 --- a/modules/nf-core/porechop/main.nf +++ b/modules/nf-core/porechop/main.nf @@ -6,7 +6,6 @@ process PORECHOP { def container_image = "porechop:0.2.4--py39h7cff6ad_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/preseq/ccurve/main.nf b/modules/nf-core/preseq/ccurve/main.nf index 6d9558765e3..9ee17f4dc77 100644 --- a/modules/nf-core/preseq/ccurve/main.nf +++ b/modules/nf-core/preseq/ccurve/main.nf @@ -7,7 +7,6 @@ process PRESEQ_CCURVE { def container_image = "preseq:3.1.2--h445547b_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index eb748dd8631..73a4e80317a 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -7,7 +7,6 @@ process PRESEQ_LCEXTRAP { def container_image = "preseq:3.1.2--h445547b_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/prinseqplusplus/main.nf b/modules/nf-core/prinseqplusplus/main.nf index d805cc590a5..2cb0c9ff0ee 100644 --- a/modules/nf-core/prinseqplusplus/main.nf +++ b/modules/nf-core/prinseqplusplus/main.nf @@ -6,7 +6,6 @@ process PRINSEQPLUSPLUS { def container_image = "prinseq-plus-plus:1.2.3--hc90279e_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index b9393612ed7..feb9605236f 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -6,7 +6,6 @@ process PRODIGAL { def container_image = "mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(genome) val(output_format) diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 108bb4559f7..47fd8be2dab 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -6,7 +6,6 @@ process PROKKA { def container_image = "prokka:1.14.6--pl5321hdfd78af_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path proteins diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index 5a7543a2fd5..a6548139540 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -6,7 +6,6 @@ process PYCOQC { def container_image = "pycoqc:2.5.2--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path summary diff --git a/modules/nf-core/pydamage/analyze/main.nf b/modules/nf-core/pydamage/analyze/main.nf index 610d8c6a798..f5b2128c975 100644 --- a/modules/nf-core/pydamage/analyze/main.nf +++ b/modules/nf-core/pydamage/analyze/main.nf @@ -6,7 +6,6 @@ process PYDAMAGE_ANALYZE { def container_image = "pydamage:0.70--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/pydamage/filter/main.nf b/modules/nf-core/pydamage/filter/main.nf index b2938e40e9a..e7fa702f533 100644 --- a/modules/nf-core/pydamage/filter/main.nf +++ b/modules/nf-core/pydamage/filter/main.nf @@ -6,7 +6,6 @@ process PYDAMAGE_FILTER { def container_image = "pydamage:0.70--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(csv) diff --git a/modules/nf-core/qcat/main.nf b/modules/nf-core/qcat/main.nf index cac598a662c..2f7f10c5e24 100644 --- a/modules/nf-core/qcat/main.nf +++ b/modules/nf-core/qcat/main.nf @@ -6,7 +6,6 @@ process QCAT { def container_image = "qcat:1.1.0--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) val barcode_kit diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 95ece0f93b0..d87a78b2b1a 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -6,7 +6,6 @@ process QUALIMAP_BAMQC { def container_image = "qualimap:2.2.2d--1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path gff diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 3ba2ac404be..957f03b5d94 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -6,7 +6,6 @@ process QUALIMAP_BAMQCCRAM { def container_image = "mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(cram), path(crai) path gff diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 0b4e1fc5432..5a3256eac1d 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -6,7 +6,6 @@ process QUALIMAP_RNASEQ { def container_image = "qualimap:2.2.2d--1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path gtf diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index 26e46f960ca..256d555b4a5 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -5,7 +5,6 @@ process QUAST { def container_image = "quast:5.2.0--py39pl5321h2add14b_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path consensus path fasta diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf index fbdee3c4bb7..0c7e9acf361 100644 --- a/modules/nf-core/racon/main.nf +++ b/modules/nf-core/racon/main.nf @@ -6,7 +6,6 @@ process RACON { def container_image = "racon:1.4.20--h9a82719_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), path(assembly), path(paf) diff --git a/modules/nf-core/rapidnj/main.nf b/modules/nf-core/rapidnj/main.nf index 81fcbe9b12e..1dd96a8152d 100644 --- a/modules/nf-core/rapidnj/main.nf +++ b/modules/nf-core/rapidnj/main.nf @@ -6,7 +6,6 @@ process RAPIDNJ { def container_image = "mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path alignment diff --git a/modules/nf-core/rasusa/main.nf b/modules/nf-core/rasusa/main.nf index aa76407633c..53f951c058d 100644 --- a/modules/nf-core/rasusa/main.nf +++ b/modules/nf-core/rasusa/main.nf @@ -6,7 +6,6 @@ process RASUSA { def container_image = "rasusa:0.3.0--h779adbc_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads), val(genome_size) val depth_cutoff diff --git a/modules/nf-core/raven/main.nf b/modules/nf-core/raven/main.nf index 37d216f887f..a0cb5355971 100644 --- a/modules/nf-core/raven/main.nf +++ b/modules/nf-core/raven/main.nf @@ -6,7 +6,6 @@ process RAVEN { def container_image = "raven-assembler:1.6.1--h2e03b76_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/raxmlng/main.nf b/modules/nf-core/raxmlng/main.nf index 890e986f7f4..03fa7e9bdbf 100644 --- a/modules/nf-core/raxmlng/main.nf +++ b/modules/nf-core/raxmlng/main.nf @@ -5,7 +5,6 @@ process RAXMLNG { def container_image = "raxml-ng:1.0.3--h32fcf60_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path alignment diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index d2f0e2997be..be9ce71a174 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -6,7 +6,6 @@ process RGI_MAIN { def container_image = "rgi:5.2.1--pyha8f3691_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 15d10476d77..c97c157fdb5 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -6,7 +6,6 @@ process RHOCALL_ANNOTATE { def container_image = "rhocall:0.5.1--py39hbf8eff0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) tuple val(meta), path(roh) diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 1dc9f3262e0..be4360b2871 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -11,7 +11,6 @@ process RMARKDOWNNOTEBOOK { def container_image = "mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0" container [ params.container_registry ?: 'quay.io/biocontainers' ,container_image ].join('/') - input: tuple val(meta), path(notebook) val parameters diff --git a/modules/nf-core/roary/main.nf b/modules/nf-core/roary/main.nf index b13dda41636..0f726087d54 100644 --- a/modules/nf-core/roary/main.nf +++ b/modules/nf-core/roary/main.nf @@ -6,7 +6,6 @@ process ROARY { def container_image = "roary:3.13.0--pl526h516909a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(gff) diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index de3b15c983c..a8862ffb873 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -6,7 +6,6 @@ process RSEM_CALCULATEEXPRESSION { def container_image = "mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 2b2a0947a6e..11cf8707bca 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -6,7 +6,6 @@ process RSEM_PREPAREREFERENCE { def container_image = "mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta, stageAs: "rsem/*" path gtf diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index 753b5f33540..f266d9eb779 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -6,7 +6,6 @@ process RSEQC_BAMSTAT { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index 8f4bffabfcb..3546eaa6814 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -6,7 +6,6 @@ process RSEQC_INFEREXPERIMENT { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path bed diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index 05c071b628b..65e7151ad1c 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -6,7 +6,6 @@ process RSEQC_INNERDISTANCE { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path bed diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index 9bb71510d7a..4efcc599393 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -6,7 +6,6 @@ process RSEQC_JUNCTIONANNOTATION { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path bed diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 38e38b96dcf..95d1f693a6b 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -6,7 +6,6 @@ process RSEQC_JUNCTIONSATURATION { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path bed diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index f3ad940aeb7..080b97e91a7 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -6,7 +6,6 @@ process RSEQC_READDISTRIBUTION { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path bed diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 22c1824dc0c..ee163006491 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -6,7 +6,6 @@ process RSEQC_READDUPLICATION { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index aa5f9cf9181..bcab5b7a114 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -6,7 +6,6 @@ process RSEQC_TIN { def container_image = "rseqc:3.0.1--py37h516909a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path bed diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index 8f9bdc1b1d6..de7eb5b37de 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -6,7 +6,6 @@ process RTGTOOLS_PEDFILTER { def container_image = "rtg-tools:3.12.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(ped) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 18b0bbf3d76..efb8125aeeb 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -6,7 +6,6 @@ process RTGTOOLS_VCFEVAL { def container_image = "rtg-tools:3.12.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(query_vcf), path(query_vcf_tbi) tuple path(truth_vcf), path(truth_vcf_tbi) @@ -51,7 +50,6 @@ process RTGTOOLS_VCFEVAL { --template=$sdf \\ --threads=$task.cpus \\ - cat <<-END_VERSIONS > versions.yml "${task.process}": rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 70e1329ed44..9233566d815 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -6,7 +6,6 @@ process SALMON_INDEX { def container_image = "salmon:1.5.2--h84f40af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path genome_fasta path transcript_fasta diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 75183bb1b7b..95e3618f8b2 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -6,7 +6,6 @@ process SALMON_QUANT { def container_image = "salmon:1.5.2--h84f40af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/samblaster/main.nf b/modules/nf-core/samblaster/main.nf index b4136e0c233..0000c99de7c 100644 --- a/modules/nf-core/samblaster/main.nf +++ b/modules/nf-core/samblaster/main.nf @@ -6,7 +6,6 @@ process SAMBLASTER { def container_image = "mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 8fe142c3614..1d4142c64c9 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_AMPLICONCLIP { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path bed diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index efd5eaa03a6..edc82bdedbb 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_BAM2FQ { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(inputbam) val split diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index c934fd9deac..88b8e1d77e8 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_COLLATE { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) path fasta diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 1bce458c081..93a881218ee 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_COLLATEFASTQ { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 97ad0ef5044..d31002680c0 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_CONVERT { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(index) path fasta diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index 1fa97e00efd..d195b07f7bb 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_DEPTH { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index a58aa52e80e..87ee7e29856 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_DICT { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index acc5259fb68..823805ea863 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_FAIDX { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 5229908e7d3..c16c949d2bc 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_FASTA { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 3768d17b369..9b88661d553 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_FASTQ { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 8a05bf265f0..ff63384dfb7 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_FIXMATE { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 472c861d435..cda0a967089 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_FLAGSTAT { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 17d2fae5d04..6f1b31a7dcd 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_GETRG { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 4960a684009..36b4a070548 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_IDXSTATS { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index adbb8a19eae..1e19da50f2f 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_INDEX { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 5f73dd24fa3..fce6b77039b 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_MARKDUP { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) path fasta diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index acb665d461c..3254bacc661 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_MERGE { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_files, stageAs: "?/*") path fasta @@ -18,7 +17,6 @@ process SAMTOOLS_MERGE { tuple val(meta), path("*.csi") , optional:true, emit: csi path "versions.yml" , emit: versions - when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 485c8d15a4f..1f668dca404 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_SORT { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 396ba12967d..020a2f3ac92 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_STATS { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index) path fasta diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index dfb8262e0be..8794aca488f 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -6,7 +6,6 @@ process SAMTOOLS_VIEW { def container_image = "samtools:1.15.1--h1170115_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(index) path fasta diff --git a/modules/nf-core/scoary/main.nf b/modules/nf-core/scoary/main.nf index c073b484f48..6b9eb0a44a7 100644 --- a/modules/nf-core/scoary/main.nf +++ b/modules/nf-core/scoary/main.nf @@ -6,7 +6,6 @@ process SCOARY { def container_image = "scoary:1.6.16--py_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(genes), path(traits) path(tree) diff --git a/modules/nf-core/scramble/clusteranalysis/main.nf b/modules/nf-core/scramble/clusteranalysis/main.nf index a734f808d4b..9ee1386092d 100644 --- a/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/modules/nf-core/scramble/clusteranalysis/main.nf @@ -6,7 +6,6 @@ process SCRAMBLE_CLUSTERANALYSIS { def container_image = "scramble:1.0.1--h779adbc_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(clusters) path fasta diff --git a/modules/nf-core/scramble/clusteridentifier/main.nf b/modules/nf-core/scramble/clusteridentifier/main.nf index 23bd7b493b3..66fb9e55b73 100644 --- a/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/modules/nf-core/scramble/clusteridentifier/main.nf @@ -6,7 +6,6 @@ process SCRAMBLE_CLUSTERIDENTIFIER { def container_image = "scramble:1.0.1--h779adbc_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index) path fasta diff --git a/modules/nf-core/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf index 625b807bf45..9a8f5a32c1d 100644 --- a/modules/nf-core/seacr/callpeak/main.nf +++ b/modules/nf-core/seacr/callpeak/main.nf @@ -7,7 +7,6 @@ process SEACR_CALLPEAK { def container_image = "mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bedgraph), path(ctrlbedgraph) val (threshold) diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf index 4e2c829fa1e..b28d4a2c1e8 100644 --- a/modules/nf-core/seqkit/pair/main.nf +++ b/modules/nf-core/seqkit/pair/main.nf @@ -6,7 +6,6 @@ process SEQKIT_PAIR { def container_image = "seqkit:2.1.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf index d6fbad78151..6a300f79843 100644 --- a/modules/nf-core/seqkit/replace/main.nf +++ b/modules/nf-core/seqkit/replace/main.nf @@ -6,7 +6,6 @@ process SEQKIT_REPLACE { def container_image = "seqkit:2.1.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf index af4c335b26b..f89e5366888 100644 --- a/modules/nf-core/seqkit/split2/main.nf +++ b/modules/nf-core/seqkit/split2/main.nf @@ -6,7 +6,6 @@ process SEQKIT_SPLIT2 { def container_image = "seqkit:2.1.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf index 1085f896b93..3ba9b8cdafb 100644 --- a/modules/nf-core/seqkit/stats/main.nf +++ b/modules/nf-core/seqkit/stats/main.nf @@ -6,7 +6,6 @@ process SEQKIT_STATS { def container_image = "seqkit:2.2.0--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqsero2/main.nf b/modules/nf-core/seqsero2/main.nf index c8a58ae3331..2b18b849a59 100644 --- a/modules/nf-core/seqsero2/main.nf +++ b/modules/nf-core/seqsero2/main.nf @@ -6,7 +6,6 @@ process SEQSERO2 { def container_image = "seqsero2:1.2.1--py_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(seqs) diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 772e439ea81..be7e7ffb027 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -6,7 +6,6 @@ process SEQTK_MERGEPE { def container_image = "seqtk:1.3--h5bf99c6_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/seqtk/rename/main.nf b/modules/nf-core/seqtk/rename/main.nf index 140fab18cb5..88b55eae404 100644 --- a/modules/nf-core/seqtk/rename/main.nf +++ b/modules/nf-core/seqtk/rename/main.nf @@ -6,7 +6,6 @@ process SEQTK_RENAME { def container_image = "seqtk:1.3--h5bf99c6_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index a71ab5a49d2..6651da42990 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -6,7 +6,6 @@ process SEQTK_SAMPLE { def container_image = "seqtk:1.3--h5bf99c6_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) val sample_size diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index 45fe7c3b519..a99d5073965 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -6,7 +6,6 @@ process SEQTK_SEQ { def container_image = "seqtk:1.3--h5bf99c6_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf index 93d4e6e0432..433f14f6705 100644 --- a/modules/nf-core/seqtk/subseq/main.nf +++ b/modules/nf-core/seqtk/subseq/main.nf @@ -6,7 +6,6 @@ process SEQTK_SUBSEQ { def container_image = "seqtk:1.3--h5bf99c6_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path sequences path filter_list diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index 163cfe392c3..7ce5c3c709a 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -6,7 +6,6 @@ process SEQUENZAUTILS_BAM2SEQZ { def container_image = "sequenza-utils:3.0.0--py38h6ed170a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(normalbam), path(tumourbam) path fasta diff --git a/modules/nf-core/sequenzautils/gcwiggle/main.nf b/modules/nf-core/sequenzautils/gcwiggle/main.nf index 55861616b9e..c42c5cd76d7 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -6,7 +6,6 @@ process SEQUENZAUTILS_GCWIGGLE { def container_image = "sequenza-utils:3.0.0--py38h6ed170a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 1243a72b707..06abe14dfd7 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -7,7 +7,6 @@ process SEQWISH_INDUCE { def container_image = "seqwish:0.7.6--h5b5514e_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(paf), path(fasta) diff --git a/modules/nf-core/seroba/run/main.nf b/modules/nf-core/seroba/run/main.nf index 2dc46c14a06..bb06f16d913 100644 --- a/modules/nf-core/seroba/run/main.nf +++ b/modules/nf-core/seroba/run/main.nf @@ -6,7 +6,6 @@ process SEROBA_RUN { def container_image = "seroba:1.0.2--pyhdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sexdeterrmine/main.nf b/modules/nf-core/sexdeterrmine/main.nf index 21a73e61110..be6ebfeaf54 100644 --- a/modules/nf-core/sexdeterrmine/main.nf +++ b/modules/nf-core/sexdeterrmine/main.nf @@ -6,7 +6,6 @@ process SEXDETERRMINE { def container_image = "sexdeterrmine:1.1.2--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(depth) path sample_list_file diff --git a/modules/nf-core/shasta/main.nf b/modules/nf-core/shasta/main.nf index 4e9ef63d788..bd8e4add09d 100644 --- a/modules/nf-core/shasta/main.nf +++ b/modules/nf-core/shasta/main.nf @@ -6,7 +6,6 @@ process SHASTA { def container_image = "shasta:0.8.0--h7d875b9_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf index a2510e4b9a1..cfe2ce894d0 100644 --- a/modules/nf-core/shasum/main.nf +++ b/modules/nf-core/shasum/main.nf @@ -6,7 +6,6 @@ process SHASUM { def container_image = "ubuntu:20.04" container [ params.container_registry ?: '' , container_image ].join('/') - input: tuple val(meta), path(file) diff --git a/modules/nf-core/shigatyper/main.nf b/modules/nf-core/shigatyper/main.nf index 4aa7c76ebbd..d055187b6d4 100644 --- a/modules/nf-core/shigatyper/main.nf +++ b/modules/nf-core/shigatyper/main.nf @@ -6,7 +6,6 @@ process SHIGATYPER { def container_image = "shigatyper:2.0.1--pyhdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf index 1f7d25e28d5..6ee183acc43 100644 --- a/modules/nf-core/shovill/main.nf +++ b/modules/nf-core/shovill/main.nf @@ -6,7 +6,6 @@ process SHOVILL { def container_image = "shovill:1.1.0--0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf index 42eadc47c5f..2d013d7f6c1 100644 --- a/modules/nf-core/sistr/main.nf +++ b/modules/nf-core/sistr/main.nf @@ -6,7 +6,6 @@ process SISTR { def container_image = "sistr_cmd:1.1.1--pyh864c0ab_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/slimfastq/main.nf b/modules/nf-core/slimfastq/main.nf index 835fb7da508..15603303c8a 100644 --- a/modules/nf-core/slimfastq/main.nf +++ b/modules/nf-core/slimfastq/main.nf @@ -7,7 +7,6 @@ process SLIMFASTQ { def container_image = "slimfastq:2.04--h87f3376_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/snapaligner/align/main.nf b/modules/nf-core/snapaligner/align/main.nf index fc5d0895625..5992a5c5f38 100644 --- a/modules/nf-core/snapaligner/align/main.nf +++ b/modules/nf-core/snapaligner/align/main.nf @@ -6,7 +6,6 @@ process SNAPALIGNER_ALIGN { def container_image = "snap-aligner:2.0.1--hd03093a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/snapaligner/index/main.nf b/modules/nf-core/snapaligner/index/main.nf index 877122911af..ba578ba5be7 100644 --- a/modules/nf-core/snapaligner/index/main.nf +++ b/modules/nf-core/snapaligner/index/main.nf @@ -6,7 +6,6 @@ process SNAPALIGNER_INDEX { def container_image = "snap-aligner:2.0.1--hd03093a_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path altcontigfile diff --git a/modules/nf-core/snippy/core/main.nf b/modules/nf-core/snippy/core/main.nf index 669e5c68da0..098929bb8cf 100644 --- a/modules/nf-core/snippy/core/main.nf +++ b/modules/nf-core/snippy/core/main.nf @@ -6,7 +6,6 @@ process SNIPPY_CORE { def container_image = "snippy:4.6.0--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(aligned_fa) path reference diff --git a/modules/nf-core/snippy/run/main.nf b/modules/nf-core/snippy/run/main.nf index 9abe5dbe634..f2f6a1ba8e1 100644 --- a/modules/nf-core/snippy/run/main.nf +++ b/modules/nf-core/snippy/run/main.nf @@ -6,7 +6,6 @@ process SNIPPY_RUN { def container_image = "snippy:4.6.0--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path reference diff --git a/modules/nf-core/snpdists/main.nf b/modules/nf-core/snpdists/main.nf index 6d450ddf230..462301dc02c 100644 --- a/modules/nf-core/snpdists/main.nf +++ b/modules/nf-core/snpdists/main.nf @@ -6,7 +6,6 @@ process SNPDISTS { def container_image = "snp-dists:0.8.2--h5bf99c6_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/snpeff/main.nf b/modules/nf-core/snpeff/main.nf index ebe7006c536..c7b53693a1b 100644 --- a/modules/nf-core/snpeff/main.nf +++ b/modules/nf-core/snpeff/main.nf @@ -6,7 +6,6 @@ process SNPEFF { def container_image = "snpeff:5.1--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) val db diff --git a/modules/nf-core/snpsift/split/main.nf b/modules/nf-core/snpsift/split/main.nf index d5a8e037e85..b34753f686f 100644 --- a/modules/nf-core/snpsift/split/main.nf +++ b/modules/nf-core/snpsift/split/main.nf @@ -6,7 +6,6 @@ process SNPSIFT_SPLIT { def container_image = "snpsift:4.3.1t--hdfd78af_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/snpsites/main.nf b/modules/nf-core/snpsites/main.nf index 7557130b292..3883ffd8572 100644 --- a/modules/nf-core/snpsites/main.nf +++ b/modules/nf-core/snpsites/main.nf @@ -5,7 +5,6 @@ process SNPSITES { def container_image = "snp-sites:2.5.1--hed695b0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path alignment diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 4f40d0675f3..85853202c6e 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -7,7 +7,6 @@ process SOMALIER_EXTRACT { def container_image = "somalier:0.2.15--h37c5b7d_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) tuple path(ref), path(refidx) diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index cffbd5321ea..0164f4e4843 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -7,7 +7,6 @@ process SOMALIER_RELATE { def container_image = "somalier:0.2.15--h37c5b7d_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(extract) path(sample_groups) diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index c3bafec266c..e7737d94d69 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -6,7 +6,6 @@ process SORTMERNA { def container_image = "sortmerna:4.3.4--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path fastas diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf index b4d4bcac3c2..668714a5932 100644 --- a/modules/nf-core/sourmash/sketch/main.nf +++ b/modules/nf-core/sourmash/sketch/main.nf @@ -6,7 +6,6 @@ process SOURMASH_SKETCH { def container_image = "sourmash:4.2.4--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index f47469e36b4..a285e2841ac 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -6,7 +6,6 @@ process SPADES { def container_image = "spades:3.15.4--h95f258a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) path hmm diff --git a/modules/nf-core/spatyper/main.nf b/modules/nf-core/spatyper/main.nf index c6031651802..43e334ffb4e 100644 --- a/modules/nf-core/spatyper/main.nf +++ b/modules/nf-core/spatyper/main.nf @@ -6,7 +6,6 @@ process SPATYPER { def container_image = "spatyper:0.3.3--pyhdfd78af_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) path repeats diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index 890ffa7ced0..63271c5438d 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -6,7 +6,6 @@ process SRATOOLS_FASTERQDUMP { def container_image = "mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(sra) path ncbi_settings diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 7d7a2fe234b..74650d14b56 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -6,7 +6,6 @@ process SRATOOLS_PREFETCH { def container_image = "sra-tools:2.11.0--pl5321ha49a11a_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), val(id) path ncbi_settings diff --git a/modules/nf-core/srst2/srst2/main.nf b/modules/nf-core/srst2/srst2/main.nf index 21d2ab8c9ef..c70aa12ac93 100644 --- a/modules/nf-core/srst2/srst2/main.nf +++ b/modules/nf-core/srst2/srst2/main.nf @@ -6,7 +6,6 @@ process SRST2_SRST2 { def container_image = "srst2:0.2.0--py27_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fastq_s), path(db) diff --git a/modules/nf-core/ssuissero/main.nf b/modules/nf-core/ssuissero/main.nf index c9e0768bab8..247f8e8f633 100644 --- a/modules/nf-core/ssuissero/main.nf +++ b/modules/nf-core/ssuissero/main.nf @@ -7,7 +7,6 @@ process SSUISSERO { def container_image = "ssuissero:1.0.1--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/stadeniolib/scramble/main.nf b/modules/nf-core/stadeniolib/scramble/main.nf index 13f40a48a7a..2bbf3732b05 100644 --- a/modules/nf-core/stadeniolib/scramble/main.nf +++ b/modules/nf-core/stadeniolib/scramble/main.nf @@ -6,7 +6,6 @@ process STADENIOLIB_SCRAMBLE { def container_image = "staden_io_lib:1.14.14--h0d9da7e_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path(fasta) diff --git a/modules/nf-core/staphopiasccmec/main.nf b/modules/nf-core/staphopiasccmec/main.nf index 754e655ca7a..a5a14c25248 100644 --- a/modules/nf-core/staphopiasccmec/main.nf +++ b/modules/nf-core/staphopiasccmec/main.nf @@ -6,7 +6,6 @@ process STAPHOPIASCCMEC { def container_image = "staphopia-sccmec:1.0.0--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index f8274f6800c..8c432e550f1 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -6,7 +6,6 @@ process STAR_ALIGN { def container_image = "mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path index diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 11abdc5d47d..75879d4a955 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -6,7 +6,6 @@ process STAR_GENOMEGENERATE { def container_image = "mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path gtf diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 1e5286ec78d..28e6b00b077 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -6,7 +6,6 @@ process STRANGER { def container_image = "stranger:0.8.1--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) path variant_catalog diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index fa8c65f5104..4218d343b1c 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -6,7 +6,6 @@ process STRELKA_GERMLINE { def container_image = "strelka:2.9.10--h9ee0642_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) path fasta diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index 1bede8664e5..16f731a2cb5 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -6,7 +6,6 @@ process STRELKA_SOMATIC { def container_image = "strelka:2.9.10--h9ee0642_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) path fasta diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 8d4c07ef76a..42a83b61046 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -6,7 +6,6 @@ process STRINGTIE_MERGE { def container_image = "stringtie:2.2.1--hecb563c_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path stringtie_gtf path annotation_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 22812ee6376..1c800e6a313 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -6,7 +6,6 @@ process STRINGTIE_STRINGTIE { def container_image = "stringtie:2.2.1--hecb563c_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) path annotation_gtf diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 9cac56cb70c..3914c53b750 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -6,7 +6,6 @@ process SUBREAD_FEATURECOUNTS { def container_image = "subread:2.0.1--hed695b0_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 0c275e8a06e..50bb1f3e173 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -5,7 +5,6 @@ process SVDB_MERGE { def container_image = "mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcfs) val (priority) diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 050fe082200..f17e6acb70e 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -6,7 +6,6 @@ process SVDB_QUERY { def container_image = "svdb:2.6.1--py39h5371cbf_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) val(in_occs) diff --git a/modules/nf-core/svtk/standardize/main.nf b/modules/nf-core/svtk/standardize/main.nf index e12bd9f45a5..abc612da252 100644 --- a/modules/nf-core/svtk/standardize/main.nf +++ b/modules/nf-core/svtk/standardize/main.nf @@ -6,7 +6,6 @@ process SVTK_STANDARDIZE { def container_image = "svtk:0.0.20190615--py37h73a75cf_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) path fasta_fai diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 0437e5ae086..b73dad84bdf 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -6,7 +6,6 @@ process TABIX_BGZIP { def container_image = "tabix:1.11--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 377ebdccd22..02e2f27f865 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -6,7 +6,6 @@ process TABIX_BGZIPTABIX { def container_image = "tabix:1.11--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index bae79766442..dec6a5796c4 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -6,7 +6,6 @@ process TABIX_TABIX { def container_image = "tabix:1.11--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tailfindr/main.nf b/modules/nf-core/tailfindr/main.nf index 30932b5470c..6a1676aa59a 100644 --- a/modules/nf-core/tailfindr/main.nf +++ b/modules/nf-core/tailfindr/main.nf @@ -6,7 +6,6 @@ process TAILFINDR { def container_image = "mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fast5) diff --git a/modules/nf-core/tbprofiler/profile/main.nf b/modules/nf-core/tbprofiler/profile/main.nf index b005e59acce..4e5a3cd9834 100644 --- a/modules/nf-core/tbprofiler/profile/main.nf +++ b/modules/nf-core/tbprofiler/profile/main.nf @@ -6,7 +6,6 @@ process TBPROFILER_PROFILE { def container_image = "tb-profiler:3.0.8--pypyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index e0f93785459..5afe63140fe 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -6,7 +6,6 @@ process TIDDIT_COV { def container_image = "tiddit:3.0.0--py39h59fae87_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input) path fasta diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 38ea627df7f..1f82efce437 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -6,7 +6,6 @@ process TIDDIT_SV { def container_image = "tiddit:3.1.0--py39h59fae87_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(input), path(input_index) path fasta diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index 48ecac9b8c1..abb12df54bb 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -6,7 +6,6 @@ process TRANSDECODER_LONGORF { def container_image = "transdecoder:5.5.0--pl5262hdfd78af_4" container [ params.container_registry ?: 'quay.io/comp-bio-aging' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index 08ae6c4c629..38d7f218c83 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -6,7 +6,6 @@ process TRANSDECODER_PREDICT { def container_image = "transdecoder:5.5.0--pl5262hdfd78af_4" container [ params.container_registry ?: 'quay.io/comp-bio-aging' , container_image ].join('/') - input: tuple val(meta), path(fasta) path(fold) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 7c76791d17f..b128500d05b 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -6,7 +6,6 @@ process TRIMGALORE { def container_image = "trim-galore:0.6.7--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 0f1dad5ab66..b64ac2d0aaf 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -6,7 +6,6 @@ process TRIMMOMATIC { def container_image = "trimmomatic:0.39--hdfd78af_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf old mode 100755 new mode 100644 index f74f4d6df1d..940652e02a7 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -7,7 +7,6 @@ process UCSC_BEDCLIP { def container_image = "ucsc-bedclip:377--h0b8a92a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bedgraph) path sizes diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 866eef98d3d..cc932590597 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -7,7 +7,6 @@ process UCSC_BEDGRAPHTOBIGWIG { def container_image = "ucsc-bedgraphtobigwig:377--h446ed27_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bedgraph) path sizes diff --git a/modules/nf-core/ucsc/bedtobigbed/main.nf b/modules/nf-core/ucsc/bedtobigbed/main.nf index afa558e97e7..5b009edb6f5 100644 --- a/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -7,7 +7,6 @@ process UCSC_BEDTOBIGBED { def container_image = "ucsc-bedtobigbed:377--ha8a8165_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path sizes diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index dc3ad8983c7..b6283de56aa 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -7,7 +7,6 @@ process UCSC_BIGWIGAVERAGEOVERBED { def container_image = "ucsc-bigwigaverageoverbed:377--h0b8a92a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path bigwig diff --git a/modules/nf-core/ucsc/liftover/main.nf b/modules/nf-core/ucsc/liftover/main.nf index d606545e92b..f94ef6bdfe0 100644 --- a/modules/nf-core/ucsc/liftover/main.nf +++ b/modules/nf-core/ucsc/liftover/main.nf @@ -7,7 +7,6 @@ process UCSC_LIFTOVER { def container_image = "ucsc-liftover:377--h0b8a92a_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bed) path(chain) diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 0156ead4ce2..8b56fb31b56 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -7,7 +7,6 @@ process UCSC_WIGTOBIGWIG { def container_image = "ucsc-wigtobigwig:377--h0b8a92a_2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(wig) path sizes diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index 7078f0ccd32..0d072ad09ba 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -6,7 +6,6 @@ process ULTRA_ALIGN { def container_image = "mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path genome diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 59b66fefc59..0b5f700a07d 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -6,7 +6,6 @@ process ULTRA_INDEX { def container_image = "ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: path fasta path gtf diff --git a/modules/nf-core/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf index c2bae6b2714..e6029054588 100644 --- a/modules/nf-core/ultra/pipeline/main.nf +++ b/modules/nf-core/ultra/pipeline/main.nf @@ -6,7 +6,6 @@ process ULTRA_PIPELINE { def container_image = "ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) path genome diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index f8501646a5f..9186305ff97 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -6,7 +6,6 @@ process UMITOOLS_DEDUP { def container_image = "umi_tools:1.1.2--py38h4a8c8d9_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) val get_output_stats diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 96d67cded0a..1436b2980e9 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -6,7 +6,6 @@ process UMITOOLS_EXTRACT { def container_image = "umi_tools:1.1.2--py38h4a8c8d9_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index c0d80106eb8..b2e3ce695f8 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -6,7 +6,6 @@ process UNICYCLER { def container_image = "unicycler:0.4.8--py38h8162308_3" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 22cc5b7a66e..6bc952d5bdc 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -6,7 +6,6 @@ process UNTAR { def container_image = "ubuntu:20.04" container [ params.container_registry ?: '' , container_image ].join('/') - input: tuple val(meta), path(archive) diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index f6a92ebd0d6..a435b8aa85b 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -6,7 +6,6 @@ process UNZIP { def container_image = "p7zip:15.09--h2d50403_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(archive) diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index a68cebbed3d..64868193561 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -6,7 +6,6 @@ process VARDICTJAVA { def container_image = "vardict-java:1.8.3--hdfd78af_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai), path(bed) path(fasta) diff --git a/modules/nf-core/variantbam/main.nf b/modules/nf-core/variantbam/main.nf index 83f3ab7b4c9..637f7522a99 100644 --- a/modules/nf-core/variantbam/main.nf +++ b/modules/nf-core/variantbam/main.nf @@ -7,7 +7,6 @@ process VARIANTBAM { def container_image = "variantbam:1.4.4a--h7d7f7ad_5" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam) diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 1406efb6c0c..97e41f142e9 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -7,7 +7,6 @@ process VCF2DB { def container_image = "vcf2db:2020.02.24--hdfd78af_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(ped) diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf index ff589d0ec51..1dfe0562174 100644 --- a/modules/nf-core/vcf2maf/main.nf +++ b/modules/nf-core/vcf2maf/main.nf @@ -8,7 +8,6 @@ process VCF2MAF { def container_image = "mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf) // Use an uncompressed VCF file! path fasta // Required diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 60d4b9e3ebe..557bd5fe7bf 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -6,7 +6,6 @@ process VCFANNO { def container_image = "vcfanno:0.3.3--h9ee0642_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) path toml diff --git a/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 7af1752dc5a..1effcad638c 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -6,7 +6,6 @@ process VCFLIB_VCFBREAKMULTI { def container_image = "vcflib:1.0.3--hecb563c_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index 263f88fefaa..45d74c5f085 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -7,7 +7,6 @@ process VCFLIB_VCFUNIQ { def container_image = "vcflib:1.0.3--hecb563c_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf index 18c11e296da..418cd58828b 100644 --- a/modules/nf-core/vcftools/main.nf +++ b/modules/nf-core/vcftools/main.nf @@ -6,7 +6,6 @@ process VCFTOOLS { def container_image = "vcftools:0.1.16--he513fc3_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional // alternative variant files, for use with the 'diff' suite of tools. diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 8f9931f56f2..216634a18d4 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -6,7 +6,6 @@ process VERIFYBAMID_VERIFYBAMID2 { def container_image = "verifybamid2:2.0.1--hbb20b25_6" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) tuple path(svd_ud), path(svd_mu), path(svd_bed) diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 0110e1eab4d..69e63117e17 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -6,7 +6,6 @@ process VSEARCH_SINTAX { def container_image = "vsearch:2.21.1--h95f258a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(queryfasta) path db diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index ea25a7f53e4..4bbedb3db83 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -6,7 +6,6 @@ process VSEARCH_USEARCHGLOBAL { def container_image = "vsearch:2.21.1--h95f258a_0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(queryfasta) path db diff --git a/modules/nf-core/wgsim/main.nf b/modules/nf-core/wgsim/main.nf index d5a0fbc6eeb..29645badae5 100644 --- a/modules/nf-core/wgsim/main.nf +++ b/modules/nf-core/wgsim/main.nf @@ -6,7 +6,6 @@ process WGSIM { def container_image = "wgsim:1.0--h5bf99c6_4" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/whamg/main.nf b/modules/nf-core/whamg/main.nf index 3de742a390c..7d0f9500c6f 100644 --- a/modules/nf-core/whamg/main.nf +++ b/modules/nf-core/whamg/main.nf @@ -6,7 +6,6 @@ process WHAMG { def container_image = "wham:1.8.0.1.2017.05.03--h8b12597_1" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(bam), path(bai) path(fasta) diff --git a/modules/nf-core/yara/index/main.nf b/modules/nf-core/yara/index/main.nf index 27cb24590ad..485042f01fd 100644 --- a/modules/nf-core/yara/index/main.nf +++ b/modules/nf-core/yara/index/main.nf @@ -6,7 +6,6 @@ process YARA_INDEX { def container_image = "yara:1.0.2--2" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf index 07a2371d2ea..48cf0acf99a 100644 --- a/modules/nf-core/yara/mapper/main.nf +++ b/modules/nf-core/yara/mapper/main.nf @@ -6,7 +6,6 @@ process YARA_MAPPER { def container_image = "mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0" container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/') - input: tuple val(meta), path(reads) tuple val(meta2), path(index)