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Bulk change conda syntax for all modules #2654

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merged 7 commits into from
Dec 13, 2022
Merged

Bulk change conda syntax for all modules #2654

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dc0de49
Add pinned conda channels
drpatelh Dec 13, 2022
5d038e8
Remove error raise for modules that dont support conda
drpatelh Dec 13, 2022
6ea938f
Add missing conda recipe
drpatelh Dec 13, 2022
b9f7c1b
Remove error raise for modules that dont support conda
drpatelh Dec 13, 2022
606e58c
Merge branch 'master' of https://github.com/nf-core/modules into conda
drpatelh Dec 13, 2022
19a92f4
Bulk change conda syntax across all modules
drpatelh Dec 13, 2022
2c158f9
Bump NF version to >=22.10.1
drpatelh Dec 13, 2022
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2 changes: 1 addition & 1 deletion modules/nf-core/abacas/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ABACAS {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null)
conda "bioconda::abacas=1.3.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
'quay.io/biocontainers/abacas:1.3.1--pl526_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/abricate/run/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ABRICATE_RUN {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
conda "bioconda::abricate=1.0.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
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@SPPearce SPPearce Dec 14, 2022 •
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Why does this have the URL encoding %3A instead of :? (And another 7 places)

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Excellent spot 👀 Not sure but it has happened before and we should probably look for it and remove in any affected modules.

'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/abricate/summary/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ABRICATE_SUMMARY {
tag "$meta.id"
label 'process_single'

conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
conda "bioconda::abricate=1.0.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/adapterremoval/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ADAPTERREMOVAL {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
conda "bioconda::adapterremoval=2.3.2"
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' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/adapterremovalfixprefix/main.nf
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Expand Up @@ -3,7 +3,7 @@ process ADAPTERREMOVALFIXPREFIX {
label 'process_single'

// 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)
conda "bioconda::adapterremovalfixprefix=0.0.5"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/agat/convertspgff2gtf/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AGAT_CONVERTSPGFF2GTF {
tag "$meta.id"
label 'process_single'

conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
conda "bioconda::agat=1.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/agat/convertspgxf2gxf/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AGAT_CONVERTSPGXF2GXF {
tag "$meta.id"
label 'process_single'

conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
conda "bioconda::agat=1.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/agat/spstatistics/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AGAT_SPSTATISTICS {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
conda "bioconda::agat=1.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/agat/sqstatbasic/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AGAT_SQSTATBASIC {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
conda "bioconda::agat=1.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/agrvate/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AGRVATE {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
conda "bioconda::agrvate=1.0.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/allelecounter/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ALLELECOUNTER {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
conda "bioconda::cancerit-allelecount=4.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ampcombi/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AMPCOMBI {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::ampcombi=0.1.7" : null)
conda "bioconda::ampcombi=0.1.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ampcombi:0.1.7--pyhdfd78af_0':
'quay.io/biocontainers/ampcombi:0.1.7--pyhdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ampir/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AMPIR {
tag "$meta.id"
label 'process_single'

conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
conda "conda-forge::r-ampir=1.1.0"
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' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/amplify/predict/main.nf
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Expand Up @@ -3,7 +3,7 @@ process AMPLIFY_PREDICT {
label 'process_single'

// 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)
conda "bioconda::amplify=1.0.3"
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' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/amps/main.nf
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@@ -1,7 +1,7 @@
process AMPS {
label 'process_low'

conda (params.enable_conda ? "bioconda::hops=0.35" : null)
conda "bioconda::hops=0.35"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/amrfinderplus/run/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AMRFINDERPLUS_RUN {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.42" : null)
conda "bioconda::ncbi-amrfinderplus=3.10.42"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0':
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/amrfinderplus/update/main.nf
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Expand Up @@ -2,7 +2,7 @@ process AMRFINDERPLUS_UPDATE {
tag "update"
label 'process_single'

conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.42" : null)
conda "bioconda::ncbi-amrfinderplus=3.10.42"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0':
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/angsd/docounts/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ANGSD_DOCOUNTS {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::angsd=0.939" : null)
conda "bioconda::angsd=0.939"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
'quay.io/biocontainers/angsd:0.939--h468462d_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/antismash/antismashlite/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ANTISMASH_ANTISMASHLITE {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
conda "bioconda::antismash-lite=6.0.1"
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' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf
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@@ -1,7 +1,7 @@
process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
label 'process_single'

conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
conda "bioconda::antismash-lite=6.0.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/arcashla/extract/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ARCASHLA_EXTRACT {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::arcas-hla=0.5.0" : null)
conda "bioconda::arcas-hla=0.5.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/arcas-hla:0.5.0--hdfd78af_0':
'quay.io/biocontainers/arcas-hla:0.5.0--hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/aria2/main.nf
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Expand Up @@ -3,7 +3,7 @@ process ARIA2 {
tag "$source_url"
label 'process_single'

conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null)
conda "conda-forge::aria2=1.36.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/aria2:1.36.0' :
'quay.io/biocontainers/aria2:1.36.0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ariba/getref/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ARIBA_GETREF {
tag "$db_name"
label 'process_low'

conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
conda "bioconda::ariba=2.14.6"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ariba/run/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ARIBA_RUN {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
conda "bioconda::ariba=2.14.6"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/arriba/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ARRIBA {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null)
conda "bioconda::arriba=2.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' :
'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/artic/guppyplex/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ARTIC_GUPPYPLEX {
tag "$meta.id"
label 'process_high'

conda (params.enable_conda ? "bioconda::artic=1.2.3" : null)
conda "bioconda::artic=1.2.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/artic/minion/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ARTIC_MINION {
tag "$meta.id"
label 'process_high'

conda (params.enable_conda ? "bioconda::artic=1.2.3" : null)
conda "bioconda::artic=1.2.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ascat/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ASCAT {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null)
conda "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0':
'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/assemblyscan/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ASSEMBLYSCAN {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null)
conda "bioconda::assembly-scan=0.4.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' :
'quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ataqv/ataqv/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ATAQV_ATAQV {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
conda "bioconda::ataqv=1.3.0"
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' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/ataqv/mkarv/main.nf
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@@ -1,7 +1,7 @@
process ATAQV_MKARV {
label 'process_medium'

conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
conda "bioconda::ataqv=1.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2':
'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/atlas/call/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ATLAS_CALL {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
conda "bioconda::atlas=0.9.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/atlas/pmd/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ATLAS_PMD {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
conda "bioconda::atlas=0.9.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/atlas/recal/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ATLAS_RECAL {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
conda "bioconda::atlas=0.9.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/atlas/splitmerge/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ATLAS_SPLITMERGE {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
conda "bioconda::atlas=0.9.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
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Expand Up @@ -2,7 +2,7 @@ process ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION {
tag "${meta.id}"
label 'process_single'

conda (params.enable_conda ? "bioconda::atlas-gene-annotation-manipulation=1.1.0" : null)
conda "bioconda::atlas-gene-annotation-manipulation=1.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0':
'quay.io/biocontainers/atlas-gene-annotation-manipulation:1.1.0--hdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bakta/bakta/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BAKTA_BAKTA {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::bakta=1.6.0" : null)
conda "bioconda::bakta=1.6.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bakta:1.6.0--pyhdfd78af_0' :
'quay.io/biocontainers/bakta:1.6.0--pyhdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bakta/baktadbdownload/main.nf
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@@ -1,7 +1,7 @@
process BAKTA_BAKTADBDOWNLOAD {
label 'process_single'

conda (params.enable_conda ? "bioconda::bakta=1.6.0" : null)
conda "bioconda::bakta=1.6.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bakta:1.6.0--pyhdfd78af_0' :
'quay.io/biocontainers/bakta:1.6.0--pyhdfd78af_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bamaligncleaner/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BAMALIGNCLEANER {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null)
conda "bioconda::bamaligncleaner=0.2.1"
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' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bamcmp/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BAMCMP {
label 'process_low'

// 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)
conda "bioconda::bamcmp=2.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bamtools/convert/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BAMTOOLS_CONVERT {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
conda "bioconda::bamtools=2.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bamtools/split/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BAMTOOLS_SPLIT {
tag "$meta.id"
label 'process_low'

conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
conda "bioconda::bamtools=2.5.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
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2 changes: 1 addition & 1 deletion modules/nf-core/bamtools/stats/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BAMTOOLS_STATS {
tag "$meta.id"
label 'process_single'

conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
conda "bioconda::bamtools=2.5.1"
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' }"
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