From 22a0afd52bb4e19f72156b09c5f59064e7eea50a Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 18:52:39 +0100 Subject: [PATCH 1/9] Move all modules to modules/nf-core/ folder --- modules/{ => nf-core}/abacas/main.nf | 0 modules/{ => nf-core}/abacas/meta.yml | 0 modules/{ => nf-core}/abricate/run/main.nf | 0 modules/{ => nf-core}/abricate/run/meta.yml | 0 modules/{ => nf-core}/abricate/summary/main.nf | 0 modules/{ => nf-core}/abricate/summary/meta.yml | 0 modules/{ => nf-core}/adapterremoval/main.nf | 0 modules/{ => nf-core}/adapterremoval/meta.yml | 0 modules/{ => nf-core}/adapterremovalfixprefix/main.nf | 0 modules/{ => nf-core}/adapterremovalfixprefix/meta.yml | 0 modules/{ => nf-core}/agrvate/main.nf | 0 modules/{ => nf-core}/agrvate/meta.yml | 0 modules/{ => nf-core}/allelecounter/main.nf | 0 modules/{ => nf-core}/allelecounter/meta.yml | 0 modules/{ => nf-core}/ampir/main.nf | 0 modules/{ => nf-core}/ampir/meta.yml | 0 modules/{ => 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from modules/homer/makeucscfile/meta.yml rename to modules/nf-core/homer/makeucscfile/meta.yml diff --git a/modules/homer/pos2bed/main.nf b/modules/nf-core/homer/pos2bed/main.nf similarity index 100% rename from modules/homer/pos2bed/main.nf rename to modules/nf-core/homer/pos2bed/main.nf diff --git a/modules/homer/pos2bed/meta.yml b/modules/nf-core/homer/pos2bed/meta.yml similarity index 100% rename from modules/homer/pos2bed/meta.yml rename to modules/nf-core/homer/pos2bed/meta.yml diff --git a/modules/hpsuissero/main.nf b/modules/nf-core/hpsuissero/main.nf similarity index 100% rename from modules/hpsuissero/main.nf rename to modules/nf-core/hpsuissero/main.nf diff --git a/modules/hpsuissero/meta.yml b/modules/nf-core/hpsuissero/meta.yml similarity index 100% rename from modules/hpsuissero/meta.yml rename to modules/nf-core/hpsuissero/meta.yml diff --git a/modules/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf similarity index 100% rename from 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a/modules/ultra/index/meta.yml b/modules/nf-core/ultra/index/meta.yml similarity index 100% rename from modules/ultra/index/meta.yml rename to modules/nf-core/ultra/index/meta.yml diff --git a/modules/ultra/pipeline/main.nf b/modules/nf-core/ultra/pipeline/main.nf similarity index 100% rename from modules/ultra/pipeline/main.nf rename to modules/nf-core/ultra/pipeline/main.nf diff --git a/modules/ultra/pipeline/meta.yml b/modules/nf-core/ultra/pipeline/meta.yml similarity index 100% rename from modules/ultra/pipeline/meta.yml rename to modules/nf-core/ultra/pipeline/meta.yml diff --git a/modules/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf similarity index 100% rename from modules/umitools/dedup/main.nf rename to modules/nf-core/umitools/dedup/main.nf diff --git a/modules/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml similarity index 100% rename from modules/umitools/dedup/meta.yml rename to modules/nf-core/umitools/dedup/meta.yml diff --git a/modules/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf similarity index 100% rename from modules/umitools/extract/main.nf rename to modules/nf-core/umitools/extract/main.nf diff --git a/modules/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml similarity index 100% rename from modules/umitools/extract/meta.yml rename to modules/nf-core/umitools/extract/meta.yml diff --git a/modules/unicycler/main.nf b/modules/nf-core/unicycler/main.nf similarity index 100% rename from modules/unicycler/main.nf rename to modules/nf-core/unicycler/main.nf diff --git a/modules/unicycler/meta.yml b/modules/nf-core/unicycler/meta.yml similarity index 100% rename from modules/unicycler/meta.yml rename to modules/nf-core/unicycler/meta.yml diff --git a/modules/untar/main.nf b/modules/nf-core/untar/main.nf similarity index 100% rename from modules/untar/main.nf rename to modules/nf-core/untar/main.nf diff --git a/modules/untar/meta.yml b/modules/nf-core/untar/meta.yml similarity index 100% rename from modules/untar/meta.yml rename to modules/nf-core/untar/meta.yml diff --git a/modules/unzip/main.nf b/modules/nf-core/unzip/main.nf similarity index 100% rename from modules/unzip/main.nf rename to modules/nf-core/unzip/main.nf diff --git a/modules/unzip/meta.yml b/modules/nf-core/unzip/meta.yml similarity index 100% rename from modules/unzip/meta.yml rename to modules/nf-core/unzip/meta.yml diff --git a/modules/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf similarity index 100% rename from modules/vardictjava/main.nf rename to modules/nf-core/vardictjava/main.nf diff --git a/modules/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml similarity index 100% rename from modules/vardictjava/meta.yml rename to modules/nf-core/vardictjava/meta.yml diff --git a/modules/variantbam/main.nf b/modules/nf-core/variantbam/main.nf similarity index 100% rename from modules/variantbam/main.nf rename to modules/nf-core/variantbam/main.nf diff --git a/modules/variantbam/meta.yml b/modules/nf-core/variantbam/meta.yml similarity index 100% rename from modules/variantbam/meta.yml rename to modules/nf-core/variantbam/meta.yml diff --git a/modules/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf similarity index 100% rename from modules/vcf2db/main.nf rename to modules/nf-core/vcf2db/main.nf diff --git a/modules/vcf2db/meta.yml b/modules/nf-core/vcf2db/meta.yml similarity index 100% rename from modules/vcf2db/meta.yml rename to modules/nf-core/vcf2db/meta.yml diff --git a/modules/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf similarity index 100% rename from modules/vcf2maf/main.nf rename to modules/nf-core/vcf2maf/main.nf diff --git a/modules/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml similarity index 100% rename from modules/vcf2maf/meta.yml rename to modules/nf-core/vcf2maf/meta.yml diff --git a/modules/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf similarity index 100% rename from modules/vcfanno/main.nf rename to modules/nf-core/vcfanno/main.nf diff --git a/modules/vcfanno/meta.yml b/modules/nf-core/vcfanno/meta.yml similarity index 100% rename from modules/vcfanno/meta.yml rename to modules/nf-core/vcfanno/meta.yml diff --git a/modules/vcflib/vcfbreakmulti/main.nf b/modules/nf-core/vcflib/vcfbreakmulti/main.nf similarity index 100% rename from modules/vcflib/vcfbreakmulti/main.nf rename to modules/nf-core/vcflib/vcfbreakmulti/main.nf diff --git a/modules/vcflib/vcfbreakmulti/meta.yml b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml similarity index 100% rename from modules/vcflib/vcfbreakmulti/meta.yml rename to modules/nf-core/vcflib/vcfbreakmulti/meta.yml diff --git a/modules/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf similarity index 100% rename from modules/vcflib/vcfuniq/main.nf rename to modules/nf-core/vcflib/vcfuniq/main.nf diff --git a/modules/vcflib/vcfuniq/meta.yml b/modules/nf-core/vcflib/vcfuniq/meta.yml similarity index 100% rename from modules/vcflib/vcfuniq/meta.yml rename to modules/nf-core/vcflib/vcfuniq/meta.yml diff --git a/modules/vcftools/main.nf b/modules/nf-core/vcftools/main.nf similarity index 100% rename from modules/vcftools/main.nf rename to modules/nf-core/vcftools/main.nf diff --git a/modules/vcftools/meta.yml b/modules/nf-core/vcftools/meta.yml similarity index 100% rename from modules/vcftools/meta.yml rename to modules/nf-core/vcftools/meta.yml diff --git a/modules/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf similarity index 100% rename from modules/vsearch/sintax/main.nf rename to modules/nf-core/vsearch/sintax/main.nf diff --git a/modules/vsearch/sintax/meta.yml b/modules/nf-core/vsearch/sintax/meta.yml similarity index 100% rename from modules/vsearch/sintax/meta.yml rename to modules/nf-core/vsearch/sintax/meta.yml diff --git a/modules/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf similarity index 100% rename from modules/vsearch/usearchglobal/main.nf rename to modules/nf-core/vsearch/usearchglobal/main.nf diff --git a/modules/vsearch/usearchglobal/meta.yml b/modules/nf-core/vsearch/usearchglobal/meta.yml similarity index 100% rename from modules/vsearch/usearchglobal/meta.yml rename to modules/nf-core/vsearch/usearchglobal/meta.yml diff --git a/modules/whamg/main.nf b/modules/nf-core/whamg/main.nf similarity index 100% rename from modules/whamg/main.nf rename to modules/nf-core/whamg/main.nf diff --git a/modules/whamg/meta.yml b/modules/nf-core/whamg/meta.yml similarity index 100% rename from modules/whamg/meta.yml rename to modules/nf-core/whamg/meta.yml diff --git a/modules/yara/index/main.nf b/modules/nf-core/yara/index/main.nf similarity index 100% rename from modules/yara/index/main.nf rename to modules/nf-core/yara/index/main.nf diff --git a/modules/yara/index/meta.yml b/modules/nf-core/yara/index/meta.yml similarity index 100% rename from modules/yara/index/meta.yml rename to modules/nf-core/yara/index/meta.yml diff --git a/modules/yara/mapper/main.nf b/modules/nf-core/yara/mapper/main.nf similarity index 100% rename from modules/yara/mapper/main.nf rename to modules/nf-core/yara/mapper/main.nf diff --git a/modules/yara/mapper/meta.yml b/modules/nf-core/yara/mapper/meta.yml similarity index 100% rename from modules/yara/mapper/meta.yml rename to modules/nf-core/yara/mapper/meta.yml From bda3df74fc436a41c71840c1526627dd8eaad1b7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 18:53:15 +0100 Subject: [PATCH 2/9] Move all tests to modules/nf-core/ folder --- tests/modules/{ => nf-core}/abacas/main.nf | 0 tests/modules/{ => nf-core}/abacas/nextflow.config | 0 tests/modules/{ => nf-core}/abacas/test.yml | 0 tests/modules/{ => nf-core}/abricate/run/main.nf | 0 tests/modules/{ => nf-core}/abricate/run/nextflow.config | 0 tests/modules/{ => nf-core}/abricate/run/test.yml | 0 tests/modules/{ => nf-core}/abricate/summary/main.nf | 0 tests/modules/{ => nf-core}/abricate/summary/nextflow.config | 0 tests/modules/{ => nf-core}/abricate/summary/test.yml | 0 tests/modules/{ => nf-core}/adapterremoval/main.nf | 0 tests/modules/{ => nf-core}/adapterremoval/nextflow.config | 0 tests/modules/{ => nf-core}/adapterremoval/test.yml | 0 tests/modules/{ => nf-core}/adapterremovalfixprefix/main.nf | 0 .../modules/{ => nf-core}/adapterremovalfixprefix/nextflow.config | 0 tests/modules/{ => nf-core}/adapterremovalfixprefix/test.yml | 0 tests/modules/{ => nf-core}/agrvate/main.nf | 0 tests/modules/{ => nf-core}/agrvate/nextflow.config | 0 tests/modules/{ => nf-core}/agrvate/test.yml | 0 tests/modules/{ => nf-core}/allelecounter/main.nf | 0 tests/modules/{ => nf-core}/allelecounter/nextflow.config | 0 tests/modules/{ => nf-core}/allelecounter/test.yml | 0 tests/modules/{ => nf-core}/ampir/main.nf | 0 tests/modules/{ => nf-core}/ampir/nextflow.config | 0 tests/modules/{ => nf-core}/ampir/test.yml | 0 tests/modules/{ => nf-core}/amplify/predict/main.nf | 0 tests/modules/{ => nf-core}/amplify/predict/nextflow.config | 0 tests/modules/{ => nf-core}/amplify/predict/test.yml | 0 tests/modules/{ => nf-core}/amps/main.nf | 0 tests/modules/{ => nf-core}/amps/nextflow.config | 0 tests/modules/{ => nf-core}/amps/test.yml | 0 tests/modules/{ => nf-core}/amrfinderplus/run/main.nf | 0 tests/modules/{ => nf-core}/amrfinderplus/run/nextflow.config | 0 tests/modules/{ => nf-core}/amrfinderplus/run/test.yml | 0 tests/modules/{ => nf-core}/amrfinderplus/update/main.nf | 0 tests/modules/{ => nf-core}/amrfinderplus/update/nextflow.config | 0 tests/modules/{ => nf-core}/amrfinderplus/update/test.yml | 0 tests/modules/{ => nf-core}/angsd/docounts/main.nf | 0 tests/modules/{ => nf-core}/angsd/docounts/nextflow.config | 0 tests/modules/{ => nf-core}/angsd/docounts/test.yml | 0 tests/modules/{ => nf-core}/antismash/antismashlite/main.nf | 0 .../modules/{ => nf-core}/antismash/antismashlite/nextflow.config | 0 tests/modules/{ => nf-core}/antismash/antismashlite/test.yml | 0 .../antismash/antismashlitedownloaddatabases/main.nf | 0 .../antismash/antismashlitedownloaddatabases/nextflow.config | 0 .../antismash/antismashlitedownloaddatabases/test.yml | 0 tests/modules/{ => nf-core}/ariba/getref/main.nf | 0 tests/modules/{ => nf-core}/ariba/getref/nextflow.config | 0 tests/modules/{ => nf-core}/ariba/getref/test.yml | 0 tests/modules/{ => nf-core}/ariba/run/main.nf | 0 tests/modules/{ => nf-core}/ariba/run/nextflow.config | 0 tests/modules/{ => nf-core}/ariba/run/test.yml | 0 tests/modules/{ => nf-core}/arriba/main.nf | 0 tests/modules/{ => nf-core}/arriba/nextflow.config | 0 tests/modules/{ => nf-core}/arriba/test.yml | 0 tests/modules/{ => nf-core}/artic/guppyplex/main.nf | 0 tests/modules/{ => nf-core}/artic/guppyplex/nextflow.config | 0 tests/modules/{ => nf-core}/artic/guppyplex/test.yml | 0 tests/modules/{ => nf-core}/artic/minion/main.nf | 0 tests/modules/{ => nf-core}/artic/minion/nextflow.config | 0 tests/modules/{ => nf-core}/artic/minion/test.yml | 0 tests/modules/{ => nf-core}/ascat/main.nf | 0 tests/modules/{ => nf-core}/ascat/nextflow.config | 0 tests/modules/{ => nf-core}/ascat/test.yml | 0 tests/modules/{ => nf-core}/assemblyscan/main.nf | 0 tests/modules/{ => nf-core}/assemblyscan/nextflow.config | 0 tests/modules/{ => nf-core}/assemblyscan/test.yml | 0 tests/modules/{ => nf-core}/ataqv/ataqv/main.nf | 0 tests/modules/{ => nf-core}/ataqv/ataqv/nextflow.config | 0 tests/modules/{ => nf-core}/ataqv/ataqv/test.yml | 0 tests/modules/{ => nf-core}/ataqv/mkarv/main.nf | 0 tests/modules/{ => nf-core}/ataqv/mkarv/nextflow.config | 0 tests/modules/{ => nf-core}/ataqv/mkarv/test.yml | 0 tests/modules/{ => nf-core}/atlas/call/main.nf | 0 tests/modules/{ => nf-core}/atlas/call/nextflow.config | 0 tests/modules/{ => nf-core}/atlas/call/test.yml | 0 tests/modules/{ => nf-core}/atlas/pmd/main.nf | 0 tests/modules/{ => nf-core}/atlas/pmd/nextflow.config | 0 tests/modules/{ => nf-core}/atlas/pmd/test.yml | 0 tests/modules/{ => nf-core}/atlas/recal/main.nf | 0 tests/modules/{ => nf-core}/atlas/recal/nextflow.config | 0 tests/modules/{ => nf-core}/atlas/recal/test.yml | 0 tests/modules/{ => nf-core}/atlas/splitmerge/main.nf | 0 tests/modules/{ => nf-core}/atlas/splitmerge/nextflow.config | 0 tests/modules/{ => nf-core}/atlas/splitmerge/test.yml | 0 tests/modules/{ => nf-core}/bakta/main.nf | 0 tests/modules/{ => nf-core}/bakta/nextflow.config | 0 tests/modules/{ => nf-core}/bakta/test.yml | 0 tests/modules/{ => nf-core}/bamaligncleaner/main.nf | 0 tests/modules/{ => nf-core}/bamaligncleaner/nextflow.config | 0 tests/modules/{ => nf-core}/bamaligncleaner/test.yml | 0 tests/modules/{ => nf-core}/bamcmp/main.nf | 0 tests/modules/{ => nf-core}/bamcmp/nextflow.config | 0 tests/modules/{ => nf-core}/bamcmp/test.yml | 0 tests/modules/{ => nf-core}/bamtools/convert/main.nf | 0 tests/modules/{ => nf-core}/bamtools/convert/nextflow.config | 0 tests/modules/{ => nf-core}/bamtools/convert/test.yml | 0 tests/modules/{ => nf-core}/bamtools/split/main.nf | 0 tests/modules/{ => nf-core}/bamtools/split/nextflow.config | 0 tests/modules/{ => nf-core}/bamtools/split/test.yml | 0 tests/modules/{ => nf-core}/bamtools/stats/main.nf | 0 tests/modules/{ => nf-core}/bamtools/stats/nextflow.config | 0 tests/modules/{ => nf-core}/bamtools/stats/test.yml | 0 tests/modules/{ => nf-core}/bamutil/trimbam/main.nf | 0 tests/modules/{ => nf-core}/bamutil/trimbam/nextflow.config | 0 tests/modules/{ => nf-core}/bamutil/trimbam/test.yml | 0 tests/modules/{ => nf-core}/bandage/image/main.nf | 0 tests/modules/{ => nf-core}/bandage/image/nextflow.config | 0 tests/modules/{ => nf-core}/bandage/image/test.yml | 0 tests/modules/{ => nf-core}/bases2fastq/main.nf | 0 tests/modules/{ => nf-core}/bases2fastq/nextflow.config | 0 tests/modules/{ => nf-core}/bases2fastq/test.yml | 0 tests/modules/{ => nf-core}/bbmap/align/main.nf | 0 tests/modules/{ => nf-core}/bbmap/align/nextflow.config | 0 tests/modules/{ => nf-core}/bbmap/align/test.yml | 0 tests/modules/{ => nf-core}/bbmap/bbduk/main.nf | 0 tests/modules/{ => nf-core}/bbmap/bbduk/nextflow.config | 0 tests/modules/{ => nf-core}/bbmap/bbduk/test.yml | 0 tests/modules/{ => nf-core}/bbmap/bbsplit/main.nf | 0 tests/modules/{ => nf-core}/bbmap/bbsplit/nextflow.config | 0 tests/modules/{ => nf-core}/bbmap/bbsplit/test.yml | 0 tests/modules/{ => nf-core}/bbmap/clumpify/main.nf | 0 tests/modules/{ => nf-core}/bbmap/clumpify/nextflow.config | 0 tests/modules/{ => nf-core}/bbmap/clumpify/test.yml | 0 tests/modules/{ => nf-core}/bbmap/index/main.nf | 0 tests/modules/{ => nf-core}/bbmap/index/nextflow.config | 0 tests/modules/{ => nf-core}/bbmap/index/test.yml | 0 tests/modules/{ => nf-core}/bbmap/pileup/main.nf | 0 tests/modules/{ => nf-core}/bbmap/pileup/nextflow.config | 0 tests/modules/{ => nf-core}/bbmap/pileup/test.yml | 0 tests/modules/{ => nf-core}/bcftools/annotate/main.nf | 0 tests/modules/{ => nf-core}/bcftools/annotate/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/annotate/test.yml | 0 tests/modules/{ => nf-core}/bcftools/concat/main.nf | 0 tests/modules/{ => nf-core}/bcftools/concat/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/concat/test.yml | 0 tests/modules/{ => nf-core}/bcftools/consensus/main.nf | 0 tests/modules/{ => nf-core}/bcftools/consensus/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/consensus/test.yml | 0 tests/modules/{ => nf-core}/bcftools/convert/main.nf | 0 tests/modules/{ => nf-core}/bcftools/convert/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/convert/test.yml | 0 tests/modules/{ => nf-core}/bcftools/filter/main.nf | 0 tests/modules/{ => nf-core}/bcftools/filter/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/filter/test.yml | 0 tests/modules/{ => nf-core}/bcftools/index/main.nf | 0 tests/modules/{ => nf-core}/bcftools/index/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/index/test.yml | 0 tests/modules/{ => nf-core}/bcftools/isec/main.nf | 0 tests/modules/{ => nf-core}/bcftools/isec/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/isec/test.yml | 0 tests/modules/{ => nf-core}/bcftools/merge/main.nf | 0 tests/modules/{ => nf-core}/bcftools/merge/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/merge/test.yml | 0 tests/modules/{ => nf-core}/bcftools/mpileup/main.nf | 0 tests/modules/{ => nf-core}/bcftools/mpileup/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/mpileup/test.yml | 0 tests/modules/{ => nf-core}/bcftools/norm/main.nf | 0 tests/modules/{ => nf-core}/bcftools/norm/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/norm/test.yml | 0 tests/modules/{ => nf-core}/bcftools/query/main.nf | 0 tests/modules/{ => nf-core}/bcftools/query/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/query/test.yml | 0 tests/modules/{ => nf-core}/bcftools/reheader/main.nf | 0 tests/modules/{ => nf-core}/bcftools/reheader/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/reheader/test.yml | 0 tests/modules/{ => nf-core}/bcftools/roh/main.nf | 0 tests/modules/{ => nf-core}/bcftools/roh/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/roh/test.yml | 0 tests/modules/{ => nf-core}/bcftools/sort/main.nf | 0 tests/modules/{ => nf-core}/bcftools/sort/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/sort/test.yml | 0 tests/modules/{ => nf-core}/bcftools/stats/main.nf | 0 tests/modules/{ => nf-core}/bcftools/stats/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/stats/test.yml | 0 tests/modules/{ => nf-core}/bcftools/view/main.nf | 0 tests/modules/{ => nf-core}/bcftools/view/nextflow.config | 0 tests/modules/{ => nf-core}/bcftools/view/test.yml | 0 tests/modules/{ => nf-core}/bcl2fastq/main.nf | 0 tests/modules/{ => nf-core}/bcl2fastq/nextflow.config | 0 tests/modules/{ => nf-core}/bcl2fastq/test.yml | 0 tests/modules/{ => nf-core}/bclconvert/main.nf | 0 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a/tests/modules/deeparg/predict/main.nf b/tests/modules/nf-core/deeparg/predict/main.nf similarity index 100% rename from tests/modules/deeparg/predict/main.nf rename to tests/modules/nf-core/deeparg/predict/main.nf diff --git a/tests/modules/deeparg/predict/nextflow.config b/tests/modules/nf-core/deeparg/predict/nextflow.config similarity index 100% rename from tests/modules/deeparg/predict/nextflow.config rename to tests/modules/nf-core/deeparg/predict/nextflow.config diff --git a/tests/modules/deeparg/predict/test.yml b/tests/modules/nf-core/deeparg/predict/test.yml similarity index 100% rename from tests/modules/deeparg/predict/test.yml rename to tests/modules/nf-core/deeparg/predict/test.yml diff --git a/tests/modules/deepbgc/download/main.nf b/tests/modules/nf-core/deepbgc/download/main.nf similarity index 100% rename from tests/modules/deepbgc/download/main.nf rename to tests/modules/nf-core/deepbgc/download/main.nf diff --git a/tests/modules/deepbgc/download/nextflow.config 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a/tests/modules/delly/call/main.nf b/tests/modules/nf-core/delly/call/main.nf similarity index 100% rename from tests/modules/delly/call/main.nf rename to tests/modules/nf-core/delly/call/main.nf diff --git a/tests/modules/delly/call/nextflow.config b/tests/modules/nf-core/delly/call/nextflow.config similarity index 100% rename from tests/modules/delly/call/nextflow.config rename to tests/modules/nf-core/delly/call/nextflow.config diff --git a/tests/modules/delly/call/test.yml b/tests/modules/nf-core/delly/call/test.yml similarity index 100% rename from tests/modules/delly/call/test.yml rename to tests/modules/nf-core/delly/call/test.yml diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/nf-core/diamond/blastp/main.nf similarity index 100% rename from tests/modules/diamond/blastp/main.nf rename to tests/modules/nf-core/diamond/blastp/main.nf diff --git a/tests/modules/diamond/blastp/nextflow.config b/tests/modules/nf-core/diamond/blastp/nextflow.config similarity index 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a/tests/modules/imputeme/vcftoprs/nextflow.config b/tests/modules/nf-core/imputeme/vcftoprs/nextflow.config similarity index 100% rename from tests/modules/imputeme/vcftoprs/nextflow.config rename to tests/modules/nf-core/imputeme/vcftoprs/nextflow.config diff --git a/tests/modules/imputeme/vcftoprs/test.yml b/tests/modules/nf-core/imputeme/vcftoprs/test.yml similarity index 100% rename from tests/modules/imputeme/vcftoprs/test.yml rename to tests/modules/nf-core/imputeme/vcftoprs/test.yml diff --git a/tests/modules/instrain/profile/main.nf b/tests/modules/nf-core/instrain/profile/main.nf similarity index 100% rename from tests/modules/instrain/profile/main.nf rename to tests/modules/nf-core/instrain/profile/main.nf diff --git a/tests/modules/instrain/profile/nextflow.config b/tests/modules/nf-core/instrain/profile/nextflow.config similarity index 100% rename from tests/modules/instrain/profile/nextflow.config rename to tests/modules/nf-core/instrain/profile/nextflow.config diff --git a/tests/modules/instrain/profile/test.yml b/tests/modules/nf-core/instrain/profile/test.yml similarity index 100% rename from tests/modules/instrain/profile/test.yml rename to tests/modules/nf-core/instrain/profile/test.yml diff --git a/tests/modules/iqtree/main.nf b/tests/modules/nf-core/iqtree/main.nf similarity index 100% rename from tests/modules/iqtree/main.nf rename to tests/modules/nf-core/iqtree/main.nf diff --git a/tests/modules/iqtree/nextflow.config b/tests/modules/nf-core/iqtree/nextflow.config similarity index 100% rename from tests/modules/iqtree/nextflow.config rename to tests/modules/nf-core/iqtree/nextflow.config diff --git a/tests/modules/iqtree/test.yml b/tests/modules/nf-core/iqtree/test.yml similarity index 100% rename from tests/modules/iqtree/test.yml rename to tests/modules/nf-core/iqtree/test.yml diff --git a/tests/modules/ismapper/main.nf b/tests/modules/nf-core/ismapper/main.nf similarity index 100% rename from tests/modules/ismapper/main.nf rename to 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a/tests/modules/isoseq3/cluster/test.yml b/tests/modules/nf-core/isoseq3/cluster/test.yml similarity index 100% rename from tests/modules/isoseq3/cluster/test.yml rename to tests/modules/nf-core/isoseq3/cluster/test.yml diff --git a/tests/modules/isoseq3/refine/main.nf b/tests/modules/nf-core/isoseq3/refine/main.nf similarity index 100% rename from tests/modules/isoseq3/refine/main.nf rename to tests/modules/nf-core/isoseq3/refine/main.nf diff --git a/tests/modules/isoseq3/refine/nextflow.config b/tests/modules/nf-core/isoseq3/refine/nextflow.config similarity index 100% rename from tests/modules/isoseq3/refine/nextflow.config rename to tests/modules/nf-core/isoseq3/refine/nextflow.config diff --git a/tests/modules/isoseq3/refine/test.yml b/tests/modules/nf-core/isoseq3/refine/test.yml similarity index 100% rename from tests/modules/isoseq3/refine/test.yml rename to tests/modules/nf-core/isoseq3/refine/test.yml diff --git a/tests/modules/ivar/consensus/main.nf 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tests/modules/ivar/trim/nextflow.config rename to tests/modules/nf-core/ivar/trim/nextflow.config diff --git a/tests/modules/ivar/trim/test.yml b/tests/modules/nf-core/ivar/trim/test.yml similarity index 100% rename from tests/modules/ivar/trim/test.yml rename to tests/modules/nf-core/ivar/trim/test.yml diff --git a/tests/modules/ivar/variants/main.nf b/tests/modules/nf-core/ivar/variants/main.nf similarity index 100% rename from tests/modules/ivar/variants/main.nf rename to tests/modules/nf-core/ivar/variants/main.nf diff --git a/tests/modules/ivar/variants/nextflow.config b/tests/modules/nf-core/ivar/variants/nextflow.config similarity index 100% rename from tests/modules/ivar/variants/nextflow.config rename to tests/modules/nf-core/ivar/variants/nextflow.config diff --git a/tests/modules/ivar/variants/test.yml b/tests/modules/nf-core/ivar/variants/test.yml similarity index 100% rename from tests/modules/ivar/variants/test.yml rename to tests/modules/nf-core/ivar/variants/test.yml diff --git a/tests/modules/jupyternotebook/main.nf b/tests/modules/nf-core/jupyternotebook/main.nf similarity index 100% rename from tests/modules/jupyternotebook/main.nf rename to tests/modules/nf-core/jupyternotebook/main.nf diff --git a/tests/modules/jupyternotebook/nextflow.config b/tests/modules/nf-core/jupyternotebook/nextflow.config similarity index 100% rename from tests/modules/jupyternotebook/nextflow.config rename to tests/modules/nf-core/jupyternotebook/nextflow.config diff --git a/tests/modules/jupyternotebook/test.yml b/tests/modules/nf-core/jupyternotebook/test.yml similarity index 100% rename from tests/modules/jupyternotebook/test.yml rename to tests/modules/nf-core/jupyternotebook/test.yml diff --git a/tests/modules/kaiju/kaiju/main.nf b/tests/modules/nf-core/kaiju/kaiju/main.nf similarity index 100% rename from tests/modules/kaiju/kaiju/main.nf rename to tests/modules/nf-core/kaiju/kaiju/main.nf diff --git a/tests/modules/kaiju/kaiju/nextflow.config b/tests/modules/nf-core/kaiju/kaiju/nextflow.config similarity index 100% rename from tests/modules/kaiju/kaiju/nextflow.config rename to tests/modules/nf-core/kaiju/kaiju/nextflow.config diff --git a/tests/modules/kaiju/kaiju/test.yml b/tests/modules/nf-core/kaiju/kaiju/test.yml similarity index 100% rename from tests/modules/kaiju/kaiju/test.yml rename to tests/modules/nf-core/kaiju/kaiju/test.yml diff --git a/tests/modules/kaiju/kaiju2krona/main.nf b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf similarity index 100% rename from tests/modules/kaiju/kaiju2krona/main.nf rename to tests/modules/nf-core/kaiju/kaiju2krona/main.nf diff --git a/tests/modules/kaiju/kaiju2krona/nextflow.config b/tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config similarity index 100% rename from tests/modules/kaiju/kaiju2krona/nextflow.config rename to tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config diff --git a/tests/modules/kaiju/kaiju2krona/test.yml b/tests/modules/nf-core/kaiju/kaiju2krona/test.yml similarity index 100% rename from tests/modules/kaiju/kaiju2krona/test.yml rename to tests/modules/nf-core/kaiju/kaiju2krona/test.yml diff --git a/tests/modules/kaiju/kaiju2table/main.nf b/tests/modules/nf-core/kaiju/kaiju2table/main.nf similarity index 100% rename from tests/modules/kaiju/kaiju2table/main.nf rename to tests/modules/nf-core/kaiju/kaiju2table/main.nf diff --git a/tests/modules/kaiju/kaiju2table/nextflow.config b/tests/modules/nf-core/kaiju/kaiju2table/nextflow.config similarity index 100% rename from tests/modules/kaiju/kaiju2table/nextflow.config rename to tests/modules/nf-core/kaiju/kaiju2table/nextflow.config diff --git a/tests/modules/kaiju/kaiju2table/test.yml b/tests/modules/nf-core/kaiju/kaiju2table/test.yml similarity index 100% rename from tests/modules/kaiju/kaiju2table/test.yml rename to tests/modules/nf-core/kaiju/kaiju2table/test.yml diff --git a/tests/modules/kallisto/index/main.nf 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a/tests/modules/khmer/normalizebymedian/main.nf b/tests/modules/nf-core/khmer/normalizebymedian/main.nf similarity index 100% rename from tests/modules/khmer/normalizebymedian/main.nf rename to tests/modules/nf-core/khmer/normalizebymedian/main.nf diff --git a/tests/modules/khmer/normalizebymedian/nextflow.config b/tests/modules/nf-core/khmer/normalizebymedian/nextflow.config similarity index 100% rename from tests/modules/khmer/normalizebymedian/nextflow.config rename to tests/modules/nf-core/khmer/normalizebymedian/nextflow.config diff --git a/tests/modules/khmer/normalizebymedian/test.yml b/tests/modules/nf-core/khmer/normalizebymedian/test.yml similarity index 100% rename from tests/modules/khmer/normalizebymedian/test.yml rename to tests/modules/nf-core/khmer/normalizebymedian/test.yml diff --git a/tests/modules/khmer/uniquekmers/main.nf b/tests/modules/nf-core/khmer/uniquekmers/main.nf similarity index 100% rename from tests/modules/khmer/uniquekmers/main.nf rename to 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rename to tests/modules/nf-core/krakentools/kreport2krona/main.nf diff --git a/tests/modules/krakentools/kreport2krona/nextflow.config b/tests/modules/nf-core/krakentools/kreport2krona/nextflow.config similarity index 100% rename from tests/modules/krakentools/kreport2krona/nextflow.config rename to tests/modules/nf-core/krakentools/kreport2krona/nextflow.config diff --git a/tests/modules/krakentools/kreport2krona/test.yml b/tests/modules/nf-core/krakentools/kreport2krona/test.yml similarity index 100% rename from tests/modules/krakentools/kreport2krona/test.yml rename to tests/modules/nf-core/krakentools/kreport2krona/test.yml diff --git a/tests/modules/krona/kronadb/main.nf b/tests/modules/nf-core/krona/kronadb/main.nf similarity index 100% rename from tests/modules/krona/kronadb/main.nf rename to tests/modules/nf-core/krona/kronadb/main.nf diff --git a/tests/modules/krona/kronadb/nextflow.config b/tests/modules/nf-core/krona/kronadb/nextflow.config similarity index 100% rename from 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b/tests/modules/nf-core/mlst/test.yml similarity index 100% rename from tests/modules/mlst/test.yml rename to tests/modules/nf-core/mlst/test.yml diff --git a/tests/modules/mobsuite/recon/main.nf b/tests/modules/nf-core/mobsuite/recon/main.nf similarity index 100% rename from tests/modules/mobsuite/recon/main.nf rename to tests/modules/nf-core/mobsuite/recon/main.nf diff --git a/tests/modules/mobsuite/recon/nextflow.config b/tests/modules/nf-core/mobsuite/recon/nextflow.config similarity index 100% rename from tests/modules/mobsuite/recon/nextflow.config rename to tests/modules/nf-core/mobsuite/recon/nextflow.config diff --git a/tests/modules/mobsuite/recon/test.yml b/tests/modules/nf-core/mobsuite/recon/test.yml similarity index 100% rename from tests/modules/mobsuite/recon/test.yml rename to tests/modules/nf-core/mobsuite/recon/test.yml diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/nf-core/mosdepth/main.nf similarity index 100% rename from tests/modules/mosdepth/main.nf 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a/tests/modules/motus/downloaddb/test.yml b/tests/modules/nf-core/motus/downloaddb/test.yml similarity index 100% rename from tests/modules/motus/downloaddb/test.yml rename to tests/modules/nf-core/motus/downloaddb/test.yml diff --git a/tests/modules/motus/merge/main.nf b/tests/modules/nf-core/motus/merge/main.nf similarity index 100% rename from tests/modules/motus/merge/main.nf rename to tests/modules/nf-core/motus/merge/main.nf diff --git a/tests/modules/motus/merge/nextflow.config b/tests/modules/nf-core/motus/merge/nextflow.config similarity index 100% rename from tests/modules/motus/merge/nextflow.config rename to tests/modules/nf-core/motus/merge/nextflow.config diff --git a/tests/modules/motus/merge/test.yml b/tests/modules/nf-core/motus/merge/test.yml similarity index 100% rename from tests/modules/motus/merge/test.yml rename to tests/modules/nf-core/motus/merge/test.yml diff --git a/tests/modules/motus/profile/main.nf b/tests/modules/nf-core/motus/profile/main.nf similarity 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rename from tests/modules/pbbam/pbmerge/test.yml rename to tests/modules/nf-core/pbbam/pbmerge/test.yml diff --git a/tests/modules/pbccs/main.nf b/tests/modules/nf-core/pbccs/main.nf similarity index 100% rename from tests/modules/pbccs/main.nf rename to tests/modules/nf-core/pbccs/main.nf diff --git a/tests/modules/pbccs/nextflow.config b/tests/modules/nf-core/pbccs/nextflow.config similarity index 100% rename from tests/modules/pbccs/nextflow.config rename to tests/modules/nf-core/pbccs/nextflow.config diff --git a/tests/modules/pbccs/test.yml b/tests/modules/nf-core/pbccs/test.yml similarity index 100% rename from tests/modules/pbccs/test.yml rename to tests/modules/nf-core/pbccs/test.yml diff --git a/tests/modules/pbptyper/main.nf b/tests/modules/nf-core/pbptyper/main.nf similarity index 100% rename from tests/modules/pbptyper/main.nf rename to tests/modules/nf-core/pbptyper/main.nf diff --git a/tests/modules/pbptyper/nextflow.config b/tests/modules/nf-core/pbptyper/nextflow.config similarity index 100% rename from tests/modules/pbptyper/nextflow.config rename to tests/modules/nf-core/pbptyper/nextflow.config diff --git a/tests/modules/pbptyper/test.yml b/tests/modules/nf-core/pbptyper/test.yml similarity index 100% rename from tests/modules/pbptyper/test.yml rename to tests/modules/nf-core/pbptyper/test.yml diff --git a/tests/modules/pear/main.nf b/tests/modules/nf-core/pear/main.nf similarity index 100% rename from tests/modules/pear/main.nf rename to tests/modules/nf-core/pear/main.nf diff --git a/tests/modules/pear/nextflow.config b/tests/modules/nf-core/pear/nextflow.config similarity index 100% rename from tests/modules/pear/nextflow.config rename to tests/modules/nf-core/pear/nextflow.config diff --git a/tests/modules/pear/test.yml b/tests/modules/nf-core/pear/test.yml similarity index 100% rename from tests/modules/pear/test.yml rename to tests/modules/nf-core/pear/test.yml diff --git a/tests/modules/peddy/main.nf b/tests/modules/nf-core/peddy/main.nf similarity index 100% rename from tests/modules/peddy/main.nf rename to tests/modules/nf-core/peddy/main.nf diff --git a/tests/modules/peddy/nextflow.config b/tests/modules/nf-core/peddy/nextflow.config similarity index 100% rename from tests/modules/peddy/nextflow.config rename to tests/modules/nf-core/peddy/nextflow.config diff --git a/tests/modules/peddy/test.yml b/tests/modules/nf-core/peddy/test.yml similarity index 100% rename from tests/modules/peddy/test.yml rename to tests/modules/nf-core/peddy/test.yml diff --git a/tests/modules/phantompeakqualtools/main.nf b/tests/modules/nf-core/phantompeakqualtools/main.nf similarity index 100% rename from tests/modules/phantompeakqualtools/main.nf rename to tests/modules/nf-core/phantompeakqualtools/main.nf diff --git a/tests/modules/phantompeakqualtools/nextflow.config b/tests/modules/nf-core/phantompeakqualtools/nextflow.config similarity index 100% rename from tests/modules/phantompeakqualtools/nextflow.config rename to 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a/tests/modules/picard/addorreplacereadgroups/main.nf b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf similarity index 100% rename from tests/modules/picard/addorreplacereadgroups/main.nf rename to tests/modules/nf-core/picard/addorreplacereadgroups/main.nf diff --git a/tests/modules/picard/addorreplacereadgroups/nextflow.config b/tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config similarity index 100% rename from tests/modules/picard/addorreplacereadgroups/nextflow.config rename to tests/modules/nf-core/picard/addorreplacereadgroups/nextflow.config diff --git a/tests/modules/picard/addorreplacereadgroups/test.yml b/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml similarity index 100% rename from tests/modules/picard/addorreplacereadgroups/test.yml rename to tests/modules/nf-core/picard/addorreplacereadgroups/test.yml diff --git a/tests/modules/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf similarity index 100% rename from tests/modules/picard/cleansam/main.nf rename to tests/modules/nf-core/picard/cleansam/main.nf diff --git a/tests/modules/picard/cleansam/nextflow.config b/tests/modules/nf-core/picard/cleansam/nextflow.config similarity index 100% rename from tests/modules/picard/cleansam/nextflow.config rename to tests/modules/nf-core/picard/cleansam/nextflow.config diff --git a/tests/modules/picard/cleansam/test.yml b/tests/modules/nf-core/picard/cleansam/test.yml similarity index 100% rename from tests/modules/picard/cleansam/test.yml rename to tests/modules/nf-core/picard/cleansam/test.yml diff --git a/tests/modules/picard/collecthsmetrics/main.nf b/tests/modules/nf-core/picard/collecthsmetrics/main.nf similarity index 100% rename from tests/modules/picard/collecthsmetrics/main.nf rename to tests/modules/nf-core/picard/collecthsmetrics/main.nf diff --git a/tests/modules/picard/collecthsmetrics/nextflow.config b/tests/modules/nf-core/picard/collecthsmetrics/nextflow.config similarity index 100% rename from tests/modules/picard/collecthsmetrics/nextflow.config rename to tests/modules/nf-core/picard/collecthsmetrics/nextflow.config diff --git a/tests/modules/picard/collecthsmetrics/test.yml b/tests/modules/nf-core/picard/collecthsmetrics/test.yml similarity index 100% rename from tests/modules/picard/collecthsmetrics/test.yml rename to tests/modules/nf-core/picard/collecthsmetrics/test.yml diff --git a/tests/modules/picard/collectmultiplemetrics/main.nf b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf similarity index 100% rename from tests/modules/picard/collectmultiplemetrics/main.nf rename to tests/modules/nf-core/picard/collectmultiplemetrics/main.nf diff --git a/tests/modules/picard/collectmultiplemetrics/nextflow.config b/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config similarity index 100% rename from tests/modules/picard/collectmultiplemetrics/nextflow.config rename to tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml similarity index 100% rename from tests/modules/picard/collectmultiplemetrics/test.yml rename to tests/modules/nf-core/picard/collectmultiplemetrics/test.yml diff --git a/tests/modules/picard/collectwgsmetrics/main.nf b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf similarity index 100% rename from tests/modules/picard/collectwgsmetrics/main.nf rename to tests/modules/nf-core/picard/collectwgsmetrics/main.nf diff --git a/tests/modules/picard/collectwgsmetrics/nextflow.config b/tests/modules/nf-core/picard/collectwgsmetrics/nextflow.config similarity index 100% rename from tests/modules/picard/collectwgsmetrics/nextflow.config rename to tests/modules/nf-core/picard/collectwgsmetrics/nextflow.config diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/nf-core/picard/collectwgsmetrics/test.yml similarity index 100% rename from tests/modules/picard/collectwgsmetrics/test.yml rename to tests/modules/nf-core/picard/collectwgsmetrics/test.yml diff --git a/tests/modules/picard/createsequencedictionary/main.nf b/tests/modules/nf-core/picard/createsequencedictionary/main.nf similarity index 100% rename from tests/modules/picard/createsequencedictionary/main.nf rename to tests/modules/nf-core/picard/createsequencedictionary/main.nf diff --git a/tests/modules/picard/createsequencedictionary/nextflow.config b/tests/modules/nf-core/picard/createsequencedictionary/nextflow.config similarity index 100% rename from tests/modules/picard/createsequencedictionary/nextflow.config rename to tests/modules/nf-core/picard/createsequencedictionary/nextflow.config diff --git a/tests/modules/picard/createsequencedictionary/test.yml b/tests/modules/nf-core/picard/createsequencedictionary/test.yml similarity index 100% rename from tests/modules/picard/createsequencedictionary/test.yml rename to tests/modules/nf-core/picard/createsequencedictionary/test.yml diff --git a/tests/modules/picard/crosscheckfingerprints/main.nf b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf similarity index 100% rename from tests/modules/picard/crosscheckfingerprints/main.nf rename to tests/modules/nf-core/picard/crosscheckfingerprints/main.nf diff --git a/tests/modules/picard/crosscheckfingerprints/nextflow.config b/tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config similarity index 100% rename from tests/modules/picard/crosscheckfingerprints/nextflow.config rename to tests/modules/nf-core/picard/crosscheckfingerprints/nextflow.config diff --git a/tests/modules/picard/crosscheckfingerprints/test.yml b/tests/modules/nf-core/picard/crosscheckfingerprints/test.yml similarity index 100% rename from tests/modules/picard/crosscheckfingerprints/test.yml rename to tests/modules/nf-core/picard/crosscheckfingerprints/test.yml diff --git a/tests/modules/picard/fastqtosam/main.nf b/tests/modules/nf-core/picard/fastqtosam/main.nf similarity index 100% rename from tests/modules/picard/fastqtosam/main.nf rename to tests/modules/nf-core/picard/fastqtosam/main.nf diff --git a/tests/modules/picard/fastqtosam/nextflow.config b/tests/modules/nf-core/picard/fastqtosam/nextflow.config similarity index 100% rename from tests/modules/picard/fastqtosam/nextflow.config rename to tests/modules/nf-core/picard/fastqtosam/nextflow.config diff --git a/tests/modules/picard/fastqtosam/test.yml b/tests/modules/nf-core/picard/fastqtosam/test.yml similarity index 100% rename from tests/modules/picard/fastqtosam/test.yml rename to tests/modules/nf-core/picard/fastqtosam/test.yml diff --git a/tests/modules/picard/filtersamreads/main.nf b/tests/modules/nf-core/picard/filtersamreads/main.nf similarity index 100% rename from tests/modules/picard/filtersamreads/main.nf rename to tests/modules/nf-core/picard/filtersamreads/main.nf diff --git a/tests/modules/picard/filtersamreads/nextflow.config b/tests/modules/nf-core/picard/filtersamreads/nextflow.config similarity index 100% rename from tests/modules/picard/filtersamreads/nextflow.config rename to tests/modules/nf-core/picard/filtersamreads/nextflow.config diff --git a/tests/modules/picard/filtersamreads/test.yml b/tests/modules/nf-core/picard/filtersamreads/test.yml similarity index 100% rename from tests/modules/picard/filtersamreads/test.yml rename to tests/modules/nf-core/picard/filtersamreads/test.yml diff --git a/tests/modules/picard/fixmateinformation/main.nf b/tests/modules/nf-core/picard/fixmateinformation/main.nf similarity index 100% rename from tests/modules/picard/fixmateinformation/main.nf rename to tests/modules/nf-core/picard/fixmateinformation/main.nf diff --git a/tests/modules/picard/fixmateinformation/nextflow.config b/tests/modules/nf-core/picard/fixmateinformation/nextflow.config similarity index 100% rename from tests/modules/picard/fixmateinformation/nextflow.config rename to tests/modules/nf-core/picard/fixmateinformation/nextflow.config diff --git a/tests/modules/picard/fixmateinformation/test.yml b/tests/modules/nf-core/picard/fixmateinformation/test.yml similarity index 100% rename from tests/modules/picard/fixmateinformation/test.yml rename to tests/modules/nf-core/picard/fixmateinformation/test.yml diff --git a/tests/modules/picard/liftovervcf/main.nf b/tests/modules/nf-core/picard/liftovervcf/main.nf similarity index 100% rename from tests/modules/picard/liftovervcf/main.nf rename to tests/modules/nf-core/picard/liftovervcf/main.nf diff --git a/tests/modules/picard/liftovervcf/nextflow.config b/tests/modules/nf-core/picard/liftovervcf/nextflow.config similarity index 100% rename from tests/modules/picard/liftovervcf/nextflow.config rename to tests/modules/nf-core/picard/liftovervcf/nextflow.config diff --git a/tests/modules/picard/liftovervcf/test.yml b/tests/modules/nf-core/picard/liftovervcf/test.yml similarity index 100% rename from tests/modules/picard/liftovervcf/test.yml rename to tests/modules/nf-core/picard/liftovervcf/test.yml diff --git a/tests/modules/picard/markduplicates/main.nf b/tests/modules/nf-core/picard/markduplicates/main.nf similarity index 100% rename from tests/modules/picard/markduplicates/main.nf rename to tests/modules/nf-core/picard/markduplicates/main.nf diff --git a/tests/modules/picard/markduplicates/nextflow.config b/tests/modules/nf-core/picard/markduplicates/nextflow.config similarity index 100% rename from tests/modules/picard/markduplicates/nextflow.config rename to tests/modules/nf-core/picard/markduplicates/nextflow.config diff --git a/tests/modules/picard/markduplicates/test.yml b/tests/modules/nf-core/picard/markduplicates/test.yml similarity index 100% rename from tests/modules/picard/markduplicates/test.yml rename to tests/modules/nf-core/picard/markduplicates/test.yml diff --git a/tests/modules/picard/mergesamfiles/main.nf b/tests/modules/nf-core/picard/mergesamfiles/main.nf similarity index 100% rename from tests/modules/picard/mergesamfiles/main.nf rename to tests/modules/nf-core/picard/mergesamfiles/main.nf diff --git a/tests/modules/picard/mergesamfiles/nextflow.config b/tests/modules/nf-core/picard/mergesamfiles/nextflow.config similarity index 100% rename from tests/modules/picard/mergesamfiles/nextflow.config rename to tests/modules/nf-core/picard/mergesamfiles/nextflow.config diff --git a/tests/modules/picard/mergesamfiles/test.yml b/tests/modules/nf-core/picard/mergesamfiles/test.yml similarity index 100% rename from tests/modules/picard/mergesamfiles/test.yml rename to tests/modules/nf-core/picard/mergesamfiles/test.yml diff --git a/tests/modules/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf similarity index 100% rename from tests/modules/picard/sortsam/main.nf rename to tests/modules/nf-core/picard/sortsam/main.nf diff --git a/tests/modules/picard/sortsam/nextflow.config b/tests/modules/nf-core/picard/sortsam/nextflow.config similarity index 100% rename from tests/modules/picard/sortsam/nextflow.config rename to tests/modules/nf-core/picard/sortsam/nextflow.config diff --git a/tests/modules/picard/sortsam/test.yml b/tests/modules/nf-core/picard/sortsam/test.yml similarity index 100% rename from tests/modules/picard/sortsam/test.yml rename to tests/modules/nf-core/picard/sortsam/test.yml diff --git a/tests/modules/picard/sortvcf/main.nf b/tests/modules/nf-core/picard/sortvcf/main.nf similarity index 100% rename from tests/modules/picard/sortvcf/main.nf rename to tests/modules/nf-core/picard/sortvcf/main.nf diff --git a/tests/modules/picard/sortvcf/nextflow.config b/tests/modules/nf-core/picard/sortvcf/nextflow.config similarity index 100% rename from tests/modules/picard/sortvcf/nextflow.config rename to tests/modules/nf-core/picard/sortvcf/nextflow.config diff --git a/tests/modules/picard/sortvcf/test.yml b/tests/modules/nf-core/picard/sortvcf/test.yml similarity index 100% rename from tests/modules/picard/sortvcf/test.yml rename to tests/modules/nf-core/picard/sortvcf/test.yml diff --git a/tests/modules/pints/caller/main.nf b/tests/modules/nf-core/pints/caller/main.nf similarity index 100% rename from tests/modules/pints/caller/main.nf rename to tests/modules/nf-core/pints/caller/main.nf diff --git a/tests/modules/pints/caller/nextflow.config b/tests/modules/nf-core/pints/caller/nextflow.config similarity index 100% rename from tests/modules/pints/caller/nextflow.config rename to tests/modules/nf-core/pints/caller/nextflow.config diff --git a/tests/modules/pints/caller/test.yml b/tests/modules/nf-core/pints/caller/test.yml similarity index 100% rename from tests/modules/pints/caller/test.yml rename to tests/modules/nf-core/pints/caller/test.yml diff --git a/tests/modules/pirate/main.nf b/tests/modules/nf-core/pirate/main.nf similarity index 100% rename from tests/modules/pirate/main.nf rename to tests/modules/nf-core/pirate/main.nf diff --git a/tests/modules/pirate/nextflow.config b/tests/modules/nf-core/pirate/nextflow.config similarity index 100% rename from tests/modules/pirate/nextflow.config rename to tests/modules/nf-core/pirate/nextflow.config diff --git a/tests/modules/pirate/test.yml b/tests/modules/nf-core/pirate/test.yml similarity index 100% rename from tests/modules/pirate/test.yml rename to tests/modules/nf-core/pirate/test.yml diff --git a/tests/modules/plasmidfinder/main.nf b/tests/modules/nf-core/plasmidfinder/main.nf similarity index 100% rename from tests/modules/plasmidfinder/main.nf rename to tests/modules/nf-core/plasmidfinder/main.nf diff --git a/tests/modules/plasmidfinder/nextflow.config b/tests/modules/nf-core/plasmidfinder/nextflow.config similarity index 100% rename from tests/modules/plasmidfinder/nextflow.config rename to tests/modules/nf-core/plasmidfinder/nextflow.config diff --git a/tests/modules/plasmidfinder/test.yml b/tests/modules/nf-core/plasmidfinder/test.yml similarity index 100% rename from tests/modules/plasmidfinder/test.yml rename to tests/modules/nf-core/plasmidfinder/test.yml diff --git a/tests/modules/plasmidid/main.nf b/tests/modules/nf-core/plasmidid/main.nf similarity index 100% rename from tests/modules/plasmidid/main.nf rename to tests/modules/nf-core/plasmidid/main.nf diff --git a/tests/modules/plasmidid/nextflow.config b/tests/modules/nf-core/plasmidid/nextflow.config similarity index 100% rename from tests/modules/plasmidid/nextflow.config rename to tests/modules/nf-core/plasmidid/nextflow.config diff --git a/tests/modules/plasmidid/test.yml b/tests/modules/nf-core/plasmidid/test.yml similarity index 100% rename from tests/modules/plasmidid/test.yml rename to tests/modules/nf-core/plasmidid/test.yml diff --git a/tests/modules/plink/extract/main.nf b/tests/modules/nf-core/plink/extract/main.nf similarity index 100% rename from tests/modules/plink/extract/main.nf rename to tests/modules/nf-core/plink/extract/main.nf diff --git a/tests/modules/plink/extract/nextflow.config b/tests/modules/nf-core/plink/extract/nextflow.config similarity index 100% rename from tests/modules/plink/extract/nextflow.config rename to tests/modules/nf-core/plink/extract/nextflow.config diff --git a/tests/modules/plink/extract/test.yml b/tests/modules/nf-core/plink/extract/test.yml similarity index 100% rename from tests/modules/plink/extract/test.yml rename to tests/modules/nf-core/plink/extract/test.yml diff --git a/tests/modules/plink/vcf/main.nf b/tests/modules/nf-core/plink/vcf/main.nf similarity index 100% rename from tests/modules/plink/vcf/main.nf rename to tests/modules/nf-core/plink/vcf/main.nf diff --git a/tests/modules/plink/vcf/nextflow.config b/tests/modules/nf-core/plink/vcf/nextflow.config similarity index 100% rename from tests/modules/plink/vcf/nextflow.config rename to tests/modules/nf-core/plink/vcf/nextflow.config diff --git a/tests/modules/plink/vcf/test.yml b/tests/modules/nf-core/plink/vcf/test.yml similarity index 100% rename from tests/modules/plink/vcf/test.yml rename to tests/modules/nf-core/plink/vcf/test.yml diff --git a/tests/modules/plink2/extract/main.nf b/tests/modules/nf-core/plink2/extract/main.nf similarity index 100% rename from tests/modules/plink2/extract/main.nf rename to tests/modules/nf-core/plink2/extract/main.nf diff --git a/tests/modules/plink2/extract/nextflow.config b/tests/modules/nf-core/plink2/extract/nextflow.config similarity index 100% rename from tests/modules/plink2/extract/nextflow.config rename to tests/modules/nf-core/plink2/extract/nextflow.config diff --git a/tests/modules/plink2/extract/test.yml b/tests/modules/nf-core/plink2/extract/test.yml similarity index 100% rename from tests/modules/plink2/extract/test.yml rename to tests/modules/nf-core/plink2/extract/test.yml diff --git a/tests/modules/plink2/score/main.nf b/tests/modules/nf-core/plink2/score/main.nf similarity index 100% rename from tests/modules/plink2/score/main.nf rename to tests/modules/nf-core/plink2/score/main.nf diff --git a/tests/modules/plink2/score/nextflow.config b/tests/modules/nf-core/plink2/score/nextflow.config similarity index 100% rename from tests/modules/plink2/score/nextflow.config rename to tests/modules/nf-core/plink2/score/nextflow.config diff --git a/tests/modules/plink2/score/test.yml b/tests/modules/nf-core/plink2/score/test.yml similarity index 100% rename from tests/modules/plink2/score/test.yml rename to tests/modules/nf-core/plink2/score/test.yml diff --git a/tests/modules/plink2/vcf/main.nf b/tests/modules/nf-core/plink2/vcf/main.nf similarity index 100% rename from tests/modules/plink2/vcf/main.nf rename to tests/modules/nf-core/plink2/vcf/main.nf diff --git a/tests/modules/plink2/vcf/nextflow.config b/tests/modules/nf-core/plink2/vcf/nextflow.config similarity index 100% rename from tests/modules/plink2/vcf/nextflow.config rename to 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a/tests/modules/porechop/main.nf b/tests/modules/nf-core/porechop/main.nf similarity index 100% rename from tests/modules/porechop/main.nf rename to tests/modules/nf-core/porechop/main.nf diff --git a/tests/modules/porechop/nextflow.config b/tests/modules/nf-core/porechop/nextflow.config similarity index 100% rename from tests/modules/porechop/nextflow.config rename to tests/modules/nf-core/porechop/nextflow.config diff --git a/tests/modules/porechop/test.yml b/tests/modules/nf-core/porechop/test.yml similarity index 100% rename from tests/modules/porechop/test.yml rename to tests/modules/nf-core/porechop/test.yml diff --git a/tests/modules/preseq/ccurve/main.nf b/tests/modules/nf-core/preseq/ccurve/main.nf similarity index 100% rename from tests/modules/preseq/ccurve/main.nf rename to tests/modules/nf-core/preseq/ccurve/main.nf diff --git a/tests/modules/preseq/ccurve/nextflow.config b/tests/modules/nf-core/preseq/ccurve/nextflow.config similarity index 100% rename from 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a/tests/modules/seqkit/stats/nextflow.config b/tests/modules/nf-core/seqkit/stats/nextflow.config similarity index 100% rename from tests/modules/seqkit/stats/nextflow.config rename to tests/modules/nf-core/seqkit/stats/nextflow.config diff --git a/tests/modules/seqkit/stats/test.yml b/tests/modules/nf-core/seqkit/stats/test.yml similarity index 100% rename from tests/modules/seqkit/stats/test.yml rename to tests/modules/nf-core/seqkit/stats/test.yml diff --git a/tests/modules/seqsero2/main.nf b/tests/modules/nf-core/seqsero2/main.nf similarity index 100% rename from tests/modules/seqsero2/main.nf rename to tests/modules/nf-core/seqsero2/main.nf diff --git a/tests/modules/seqsero2/nextflow.config b/tests/modules/nf-core/seqsero2/nextflow.config similarity index 100% rename from tests/modules/seqsero2/nextflow.config rename to tests/modules/nf-core/seqsero2/nextflow.config diff --git a/tests/modules/seqsero2/test.yml b/tests/modules/nf-core/seqsero2/test.yml similarity index 100% rename from tests/modules/seqsero2/test.yml rename to tests/modules/nf-core/seqsero2/test.yml diff --git a/tests/modules/seqtk/mergepe/main.nf b/tests/modules/nf-core/seqtk/mergepe/main.nf similarity index 100% rename from tests/modules/seqtk/mergepe/main.nf rename to tests/modules/nf-core/seqtk/mergepe/main.nf diff --git a/tests/modules/seqtk/mergepe/nextflow.config b/tests/modules/nf-core/seqtk/mergepe/nextflow.config similarity index 100% rename from tests/modules/seqtk/mergepe/nextflow.config rename to tests/modules/nf-core/seqtk/mergepe/nextflow.config diff --git a/tests/modules/seqtk/mergepe/test.yml b/tests/modules/nf-core/seqtk/mergepe/test.yml similarity index 100% rename from tests/modules/seqtk/mergepe/test.yml rename to tests/modules/nf-core/seqtk/mergepe/test.yml diff --git a/tests/modules/seqtk/rename/main.nf b/tests/modules/nf-core/seqtk/rename/main.nf similarity index 100% rename from tests/modules/seqtk/rename/main.nf rename to tests/modules/nf-core/seqtk/rename/main.nf diff 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from tests/modules/spatyper/test.yml rename to tests/modules/nf-core/spatyper/test.yml diff --git a/tests/modules/sratools/fasterqdump/main.nf b/tests/modules/nf-core/sratools/fasterqdump/main.nf similarity index 100% rename from tests/modules/sratools/fasterqdump/main.nf rename to tests/modules/nf-core/sratools/fasterqdump/main.nf diff --git a/tests/modules/sratools/fasterqdump/nextflow.config b/tests/modules/nf-core/sratools/fasterqdump/nextflow.config similarity index 100% rename from tests/modules/sratools/fasterqdump/nextflow.config rename to tests/modules/nf-core/sratools/fasterqdump/nextflow.config diff --git a/tests/modules/sratools/fasterqdump/test.yml b/tests/modules/nf-core/sratools/fasterqdump/test.yml similarity index 100% rename from tests/modules/sratools/fasterqdump/test.yml rename to tests/modules/nf-core/sratools/fasterqdump/test.yml diff --git a/tests/modules/sratools/prefetch/main.nf b/tests/modules/nf-core/sratools/prefetch/main.nf similarity index 100% rename from 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rename to tests/modules/nf-core/srst2/srst2/nextflow.config diff --git a/tests/modules/srst2/srst2/test.yml b/tests/modules/nf-core/srst2/srst2/test.yml similarity index 100% rename from tests/modules/srst2/srst2/test.yml rename to tests/modules/nf-core/srst2/srst2/test.yml diff --git a/tests/modules/ssuissero/main.nf b/tests/modules/nf-core/ssuissero/main.nf similarity index 100% rename from tests/modules/ssuissero/main.nf rename to tests/modules/nf-core/ssuissero/main.nf diff --git a/tests/modules/ssuissero/nextflow.config b/tests/modules/nf-core/ssuissero/nextflow.config similarity index 100% rename from tests/modules/ssuissero/nextflow.config rename to tests/modules/nf-core/ssuissero/nextflow.config diff --git a/tests/modules/ssuissero/test.yml b/tests/modules/nf-core/ssuissero/test.yml similarity index 100% rename from tests/modules/ssuissero/test.yml rename to tests/modules/nf-core/ssuissero/test.yml diff --git a/tests/modules/stadeniolib/scramble/main.nf 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tests/modules/vsearch/usearchglobal/test.yml rename to tests/modules/nf-core/vsearch/usearchglobal/test.yml diff --git a/tests/modules/whamg/main.nf b/tests/modules/nf-core/whamg/main.nf similarity index 100% rename from tests/modules/whamg/main.nf rename to tests/modules/nf-core/whamg/main.nf diff --git a/tests/modules/whamg/nextflow.config b/tests/modules/nf-core/whamg/nextflow.config similarity index 100% rename from tests/modules/whamg/nextflow.config rename to tests/modules/nf-core/whamg/nextflow.config diff --git a/tests/modules/whamg/test.yml b/tests/modules/nf-core/whamg/test.yml similarity index 100% rename from tests/modules/whamg/test.yml rename to tests/modules/nf-core/whamg/test.yml diff --git a/tests/modules/yara/index/main.nf b/tests/modules/nf-core/yara/index/main.nf similarity index 100% rename from tests/modules/yara/index/main.nf rename to tests/modules/nf-core/yara/index/main.nf diff --git a/tests/modules/yara/index/nextflow.config b/tests/modules/nf-core/yara/index/nextflow.config similarity index 100% rename from tests/modules/yara/index/nextflow.config rename to tests/modules/nf-core/yara/index/nextflow.config diff --git a/tests/modules/yara/index/test.yml b/tests/modules/nf-core/yara/index/test.yml similarity index 100% rename from tests/modules/yara/index/test.yml rename to tests/modules/nf-core/yara/index/test.yml diff --git a/tests/modules/yara/mapper/main.nf b/tests/modules/nf-core/yara/mapper/main.nf similarity index 100% rename from tests/modules/yara/mapper/main.nf rename to tests/modules/nf-core/yara/mapper/main.nf diff --git a/tests/modules/yara/mapper/nextflow.config b/tests/modules/nf-core/yara/mapper/nextflow.config similarity index 100% rename from tests/modules/yara/mapper/nextflow.config rename to tests/modules/nf-core/yara/mapper/nextflow.config diff --git a/tests/modules/yara/mapper/test.yml b/tests/modules/nf-core/yara/mapper/test.yml similarity index 100% rename from tests/modules/yara/mapper/test.yml rename to tests/modules/nf-core/yara/mapper/test.yml From bddd9dee8c4e74dbf9803715e71f17751001120f Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 18:58:54 +0100 Subject: [PATCH 3/9] Replace relative paths in modules test main scripts --- tests/modules/nf-core/abacas/main.nf | 2 +- tests/modules/nf-core/abricate/run/main.nf | 2 +- tests/modules/nf-core/abricate/summary/main.nf | 4 ++-- tests/modules/nf-core/adapterremoval/main.nf | 4 ++-- .../nf-core/adapterremovalfixprefix/main.nf | 4 ++-- tests/modules/nf-core/agrvate/main.nf | 2 +- tests/modules/nf-core/allelecounter/main.nf | 2 +- tests/modules/nf-core/ampir/main.nf | 2 +- tests/modules/nf-core/amplify/predict/main.nf | 4 ++-- tests/modules/nf-core/amps/main.nf | 12 ++++++------ .../modules/nf-core/amrfinderplus/run/main.nf | 4 ++-- .../nf-core/amrfinderplus/update/main.nf | 2 +- tests/modules/nf-core/angsd/docounts/main.nf | 2 +- .../nf-core/antismash/antismashlite/main.nf | 14 +++++++------- .../antismashlitedownloaddatabases/main.nf | 8 ++++---- tests/modules/nf-core/ariba/getref/main.nf | 2 +- tests/modules/nf-core/ariba/run/main.nf | 4 ++-- tests/modules/nf-core/arriba/main.nf | 6 +++--- tests/modules/nf-core/artic/guppyplex/main.nf | 2 +- tests/modules/nf-core/artic/minion/main.nf | 4 ++-- tests/modules/nf-core/ascat/main.nf | 14 +++++++------- tests/modules/nf-core/assemblyscan/main.nf | 2 +- tests/modules/nf-core/ataqv/ataqv/main.nf | 4 ++-- tests/modules/nf-core/ataqv/mkarv/main.nf | 4 ++-- tests/modules/nf-core/atlas/call/main.nf | 2 +- tests/modules/nf-core/atlas/pmd/main.nf | 2 +- tests/modules/nf-core/atlas/recal/main.nf | 2 +- tests/modules/nf-core/atlas/splitmerge/main.nf | 2 +- tests/modules/nf-core/bakta/main.nf | 2 +- tests/modules/nf-core/bamaligncleaner/main.nf | 2 +- tests/modules/nf-core/bamcmp/main.nf | 14 +++++++------- tests/modules/nf-core/bamtools/convert/main.nf | 18 +++++++++--------- tests/modules/nf-core/bamtools/split/main.nf | 4 ++-- tests/modules/nf-core/bamtools/stats/main.nf | 2 +- tests/modules/nf-core/bamutil/trimbam/main.nf | 2 +- tests/modules/nf-core/bandage/image/main.nf | 2 +- tests/modules/nf-core/bases2fastq/main.nf | 4 ++-- tests/modules/nf-core/bbmap/align/main.nf | 6 +++--- tests/modules/nf-core/bbmap/bbduk/main.nf | 2 +- tests/modules/nf-core/bbmap/bbsplit/main.nf | 4 ++-- tests/modules/nf-core/bbmap/clumpify/main.nf | 2 +- tests/modules/nf-core/bbmap/index/main.nf | 2 +- tests/modules/nf-core/bbmap/pileup/main.nf | 2 +- .../modules/nf-core/bcftools/annotate/main.nf | 2 +- tests/modules/nf-core/bcftools/concat/main.nf | 2 +- .../modules/nf-core/bcftools/consensus/main.nf | 2 +- tests/modules/nf-core/bcftools/convert/main.nf | 4 ++-- tests/modules/nf-core/bcftools/filter/main.nf | 2 +- tests/modules/nf-core/bcftools/index/main.nf | 4 ++-- tests/modules/nf-core/bcftools/isec/main.nf | 2 +- tests/modules/nf-core/bcftools/merge/main.nf | 6 +++--- tests/modules/nf-core/bcftools/mpileup/main.nf | 2 +- tests/modules/nf-core/bcftools/norm/main.nf | 2 +- tests/modules/nf-core/bcftools/query/main.nf | 2 +- .../modules/nf-core/bcftools/reheader/main.nf | 2 +- tests/modules/nf-core/bcftools/roh/main.nf | 2 +- tests/modules/nf-core/bcftools/sort/main.nf | 2 +- tests/modules/nf-core/bcftools/stats/main.nf | 2 +- tests/modules/nf-core/bcftools/view/main.nf | 2 +- tests/modules/nf-core/bcl2fastq/main.nf | 4 ++-- tests/modules/nf-core/bclconvert/main.nf | 4 ++-- .../modules/nf-core/bedtools/bamtobed/main.nf | 2 +- .../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 +- .../nf-core/bedtools/makewindows/main.nf | 2 +- .../modules/nf-core/bedtools/maskfasta/main.nf | 2 +- tests/modules/nf-core/bedtools/merge/main.nf | 2 +- tests/modules/nf-core/bedtools/slop/main.nf | 2 +- tests/modules/nf-core/bedtools/sort/main.nf | 2 +- tests/modules/nf-core/bedtools/split/main.nf | 2 +- .../modules/nf-core/bedtools/subtract/main.nf | 2 +- .../biobambam/bammarkduplicates2/main.nf | 2 +- .../modules/nf-core/biobambam/bammerge/main.nf | 2 +- .../nf-core/biobambam/bamsormadup/main.nf | 2 +- tests/modules/nf-core/biscuit/align/main.nf | 6 +++--- .../nf-core/biscuit/biscuitblaster/main.nf | 6 +++--- tests/modules/nf-core/biscuit/bsconv/main.nf | 4 ++-- tests/modules/nf-core/biscuit/epiread/main.nf | 4 ++-- tests/modules/nf-core/biscuit/index/main.nf | 2 +- tests/modules/nf-core/biscuit/mergecg/main.nf | 4 ++-- tests/modules/nf-core/biscuit/pileup/main.nf | 4 ++-- tests/modules/nf-core/biscuit/qc/main.nf | 4 ++-- tests/modules/nf-core/biscuit/vcf2bed/main.nf | 2 +- tests/modules/nf-core/bismark/align/main.nf | 6 +++--- .../nf-core/bismark/deduplicate/main.nf | 2 +- .../nf-core/bismark/genomepreparation/main.nf | 2 +- .../bismark/methylationextractor/main.nf | 4 ++-- tests/modules/nf-core/bismark/report/main.nf | 10 +++++----- tests/modules/nf-core/bismark/summary/main.nf | 10 +++++----- tests/modules/nf-core/blast/blastn/main.nf | 4 ++-- .../modules/nf-core/blast/makeblastdb/main.nf | 2 +- tests/modules/nf-core/blast/tblastn/main.nf | 4 ++-- tests/modules/nf-core/bowtie/align/main.nf | 4 ++-- .../modules/nf-core/bowtie/build_test/main.nf | 2 +- tests/modules/nf-core/bowtie2/align/main.nf | 4 ++-- .../modules/nf-core/bowtie2/build_test/main.nf | 2 +- tests/modules/nf-core/bracken/bracken/main.nf | 6 +++--- .../bracken/combinebrackenoutputs/main.nf | 8 ++++---- tests/modules/nf-core/busco/main.nf | 2 +- tests/modules/nf-core/bwa/aln/main.nf | 4 ++-- tests/modules/nf-core/bwa/index/main.nf | 2 +- tests/modules/nf-core/bwa/mem/main.nf | 4 ++-- tests/modules/nf-core/bwa/sampe/main.nf | 6 +++--- tests/modules/nf-core/bwa/samse/main.nf | 6 +++--- tests/modules/nf-core/bwamem2/index/main.nf | 2 +- tests/modules/nf-core/bwamem2/mem/main.nf | 4 ++-- tests/modules/nf-core/bwameth/align/main.nf | 4 ++-- tests/modules/nf-core/bwameth/index/main.nf | 2 +- tests/modules/nf-core/cat/cat/main.nf | 6 +++--- tests/modules/nf-core/cat/fastq/main.nf | 2 +- tests/modules/nf-core/cellranger/count/main.nf | 6 +++--- .../modules/nf-core/cellranger/mkfastq/main.nf | 4 ++-- tests/modules/nf-core/cellranger/mkgtf/main.nf | 2 +- tests/modules/nf-core/cellranger/mkref/main.nf | 2 +- .../nf-core/centrifuge/centrifuge/main.nf | 4 ++-- .../modules/nf-core/centrifuge/kreport/main.nf | 6 +++--- tests/modules/nf-core/checkm/lineagewf/main.nf | 2 +- tests/modules/nf-core/checkm/qa/main.nf | 8 ++++---- tests/modules/nf-core/chromap/chromap/main.nf | 6 +++--- tests/modules/nf-core/chromap/index/main.nf | 2 +- tests/modules/nf-core/clonalframeml/main.nf | 2 +- tests/modules/nf-core/cmseq/polymut/main.nf | 2 +- .../modules/nf-core/cnvkit/antitarget/main.nf | 2 +- tests/modules/nf-core/cnvkit/batch/main.nf | 8 ++++---- tests/modules/nf-core/cnvkit/reference/main.nf | 2 +- .../modules/nf-core/cnvpytor/callcnvs/main.nf | 2 +- .../modules/nf-core/cnvpytor/histogram/main.nf | 2 +- .../nf-core/cnvpytor/importreaddepth/main.nf | 2 +- .../modules/nf-core/cnvpytor/partition/main.nf | 2 +- tests/modules/nf-core/cnvpytor/view/main.nf | 2 +- .../controlfreec/assesssignificance/main.nf | 6 +++--- .../modules/nf-core/controlfreec/freec/main.nf | 4 ++-- .../nf-core/controlfreec/freec2bed/main.nf | 6 +++--- .../nf-core/controlfreec/freec2circos/main.nf | 6 +++--- .../nf-core/controlfreec/makegraph/main.nf | 6 +++--- tests/modules/nf-core/cooler/cload/main.nf | 12 ++++++------ tests/modules/nf-core/cooler/digest/main.nf | 2 +- tests/modules/nf-core/cooler/dump/main.nf | 2 +- tests/modules/nf-core/cooler/merge/main.nf | 4 ++-- tests/modules/nf-core/cooler/zoomify/main.nf | 2 +- tests/modules/nf-core/csvtk/concat/main.nf | 2 +- tests/modules/nf-core/csvtk/split/main.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +++--- .../nf-core/custom/getchromsizes/main.nf | 2 +- .../custom/sratoolsncbisettings/main.nf | 2 +- tests/modules/nf-core/cutadapt/main.nf | 2 +- tests/modules/nf-core/damageprofiler/main.nf | 2 +- tests/modules/nf-core/dastool/dastool/main.nf | 8 ++++---- .../nf-core/dastool/fastatocontig2bin/main.nf | 8 ++++---- .../nf-core/dastool/scaffolds2bin/main.nf | 8 ++++---- tests/modules/nf-core/dedup/main.nf | 2 +- .../nf-core/deeparg/downloaddata/main.nf | 2 +- tests/modules/nf-core/deeparg/predict/main.nf | 4 ++-- tests/modules/nf-core/deepbgc/download/main.nf | 2 +- tests/modules/nf-core/deepbgc/pipeline/main.nf | 8 ++++---- .../nf-core/deeptools/bamcoverage/main.nf | 2 +- .../nf-core/deeptools/computematrix/main.nf | 2 +- .../nf-core/deeptools/plotfingerprint/main.nf | 2 +- .../nf-core/deeptools/plotheatmap/main.nf | 2 +- .../nf-core/deeptools/plotprofile/main.nf | 2 +- tests/modules/nf-core/deepvariant/main.nf | 4 ++-- tests/modules/nf-core/delly/call/main.nf | 2 +- tests/modules/nf-core/diamond/blastp/main.nf | 4 ++-- tests/modules/nf-core/diamond/blastx/main.nf | 4 ++-- tests/modules/nf-core/diamond/makedb/main.nf | 2 +- tests/modules/nf-core/dragmap/align/main.nf | 4 ++-- .../modules/nf-core/dragmap/hashtable/main.nf | 2 +- tests/modules/nf-core/dragonflye/main.nf | 4 ++-- .../nf-core/dshbio/exportsegments/main.nf | 2 +- tests/modules/nf-core/dshbio/filterbed/main.nf | 2 +- .../modules/nf-core/dshbio/filtergff3/main.nf | 2 +- tests/modules/nf-core/dshbio/splitbed/main.nf | 2 +- tests/modules/nf-core/dshbio/splitgff3/main.nf | 2 +- tests/modules/nf-core/ectyper/main.nf | 2 +- tests/modules/nf-core/eido/convert/main.nf | 2 +- tests/modules/nf-core/eido/validate/main.nf | 2 +- tests/modules/nf-core/elprep/filter/main.nf | 2 +- tests/modules/nf-core/elprep/merge/main.nf | 4 ++-- tests/modules/nf-core/elprep/split/main.nf | 2 +- tests/modules/nf-core/emboss/seqret/main.nf | 4 ++-- tests/modules/nf-core/emmtyper/main.nf | 2 +- tests/modules/nf-core/endorspy/main.nf | 10 +++++----- tests/modules/nf-core/ensemblvep/main.nf | 12 ++++++------ .../nf-core/entrezdirect/esummary/main.nf | 2 +- .../nf-core/entrezdirect/xtract/main.nf | 4 ++-- tests/modules/nf-core/epang/main.nf | 2 +- tests/modules/nf-core/expansionhunter/main.nf | 2 +- tests/modules/nf-core/faqcs/main.nf | 2 +- tests/modules/nf-core/fargene/main.nf | 4 ++-- tests/modules/nf-core/fastani/main.nf | 2 +- tests/modules/nf-core/fastawindows/main.nf | 2 +- tests/modules/nf-core/fastk/fastk/main.nf | 2 +- tests/modules/nf-core/fastk/histex/main.nf | 4 ++-- tests/modules/nf-core/fastk/merge/main.nf | 4 ++-- tests/modules/nf-core/fastp/main.nf | 2 +- tests/modules/nf-core/fastqc/main.nf | 2 +- tests/modules/nf-core/fastqscan/main.nf | 2 +- tests/modules/nf-core/fasttree/main.nf | 2 +- tests/modules/nf-core/fcs/fcsadaptor/main.nf | 2 +- tests/modules/nf-core/ffq/main.nf | 2 +- .../fgbio/callmolecularconsensusreads/main.nf | 4 ++-- tests/modules/nf-core/fgbio/fastqtobam/main.nf | 2 +- .../nf-core/fgbio/groupreadsbyumi/main.nf | 2 +- tests/modules/nf-core/fgbio/sortbam/main.nf | 2 +- tests/modules/nf-core/filtlong/main.nf | 2 +- tests/modules/nf-core/flash/main.nf | 2 +- tests/modules/nf-core/flye/main.nf | 2 +- tests/modules/nf-core/fq/lint/main.nf | 2 +- tests/modules/nf-core/freebayes/main.nf | 2 +- tests/modules/nf-core/gamma/gamma/main.nf | 2 +- .../nf-core/gappa/examineassign/main.nf | 2 +- .../modules/nf-core/gappa/examinegraft/main.nf | 2 +- .../nf-core/gappa/examineheattree/main.nf | 2 +- .../nf-core/gatk/indelrealigner/main.nf | 4 ++-- .../gatk/realignertargetcreator/main.nf | 2 +- .../nf-core/gatk/unifiedgenotyper/main.nf | 2 +- tests/modules/nf-core/gatk4/applybqsr/main.nf | 2 +- .../nf-core/gatk4/applybqsrspark/main.nf | 2 +- tests/modules/nf-core/gatk4/applyvqsr/main.nf | 4 ++-- .../nf-core/gatk4/baserecalibrator/main.nf | 2 +- .../gatk4/baserecalibratorspark/main.nf | 2 +- .../nf-core/gatk4/bedtointervallist/main.nf | 2 +- .../gatk4/calculatecontamination/main.nf | 4 ++-- .../gatk4/calibratedragstrmodel/main.nf | 2 +- .../nf-core/gatk4/cnnscorevariants/main.nf | 2 +- .../nf-core/gatk4/collectreadcounts/main.nf | 2 +- .../nf-core/gatk4/collectsvevidence/main.nf | 2 +- .../modules/nf-core/gatk4/combinegvcfs/main.nf | 2 +- .../nf-core/gatk4/composestrtablefile/main.nf | 2 +- .../gatk4/createsequencedictionary/main.nf | 2 +- .../gatk4/createsomaticpanelofnormals/main.nf | 4 ++-- .../gatk4/estimatelibrarycomplexity/main.nf | 2 +- tests/modules/nf-core/gatk4/fastqtosam/main.nf | 2 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 2 +- .../gatk4/filtervarianttranches/main.nf | 6 +++--- .../nf-core/gatk4/gatherbqsrreports/main.nf | 2 +- .../gatk4/gatherpileupsummaries/main.nf | 2 +- .../nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- .../nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- .../nf-core/gatk4/getpileupsummaries/main.nf | 2 +- .../nf-core/gatk4/haplotypecaller/main.nf | 2 +- .../nf-core/gatk4/indexfeaturefile/main.nf | 2 +- .../nf-core/gatk4/intervallisttobed/main.nf | 2 +- .../nf-core/gatk4/intervallisttools/main.nf | 4 ++-- .../gatk4/learnreadorientationmodel/main.nf | 2 +- .../gatk4/leftalignandtrimvariants/main.nf | 2 +- .../nf-core/gatk4/markduplicates/main.nf | 4 ++-- .../nf-core/gatk4/markduplicatesspark/main.nf | 6 +++--- .../nf-core/gatk4/mergebamalignment/main.nf | 2 +- .../nf-core/gatk4/mergemutectstats/main.nf | 2 +- tests/modules/nf-core/gatk4/mergevcfs/main.nf | 2 +- tests/modules/nf-core/gatk4/mutect2/main.nf | 8 ++++---- .../nf-core/gatk4/printsvevidence/main.nf | 6 +++--- .../modules/nf-core/gatk4/reblockgvcf/main.nf | 2 +- tests/modules/nf-core/gatk4/revertsam/main.nf | 2 +- tests/modules/nf-core/gatk4/samtofastq/main.nf | 2 +- .../nf-core/gatk4/selectvariants/main.nf | 2 +- .../nf-core/gatk4/splitintervals/main.nf | 2 +- .../nf-core/gatk4/splitncigarreads/main.nf | 2 +- .../nf-core/gatk4/variantfiltration/main.nf | 2 +- .../nf-core/gatk4/variantrecalibrator/main.nf | 4 ++-- tests/modules/nf-core/gecco/run/main.nf | 2 +- tests/modules/nf-core/genescopefk/main.nf | 6 +++--- tests/modules/nf-core/genmap/index/main.nf | 2 +- .../modules/nf-core/genmap/mappability/main.nf | 4 ++-- tests/modules/nf-core/genmod/annotate/main.nf | 2 +- tests/modules/nf-core/genmod/compound/main.nf | 2 +- tests/modules/nf-core/genmod/models/main.nf | 2 +- tests/modules/nf-core/genmod/score/main.nf | 2 +- tests/modules/nf-core/genomescope2/main.nf | 6 +++--- tests/modules/nf-core/genotyphi/parse/main.nf | 4 ++-- tests/modules/nf-core/genrich/main.nf | 8 ++++---- tests/modules/nf-core/gfaffix/main.nf | 2 +- tests/modules/nf-core/gffread/main.nf | 2 +- tests/modules/nf-core/glimpse/chunk/main.nf | 2 +- tests/modules/nf-core/glnexus/main.nf | 2 +- tests/modules/nf-core/goat/taxonsearch/main.nf | 2 +- tests/modules/nf-core/graphmap2/align/main.nf | 4 ++-- tests/modules/nf-core/graphmap2/index/main.nf | 2 +- tests/modules/nf-core/gstama/collapse/main.nf | 2 +- tests/modules/nf-core/gstama/merge/main.nf | 2 +- .../nf-core/gstama/polyacleanup/main.nf | 2 +- .../modules/nf-core/gtdbtk/classifywf/main.nf | 2 +- tests/modules/nf-core/gubbins/main.nf | 2 +- tests/modules/nf-core/gunc/downloaddb/main.nf | 2 +- tests/modules/nf-core/gunc/run/main.nf | 4 ++-- tests/modules/nf-core/gunzip/main.nf | 2 +- .../nf-core/gvcftools/extractvariants/main.nf | 2 +- .../nf-core/hamronization/abricate/main.nf | 2 +- .../hamronization/amrfinderplus/main.nf | 2 +- .../nf-core/hamronization/deeparg/main.nf | 2 +- .../nf-core/hamronization/fargene/main.nf | 6 +++--- .../modules/nf-core/hamronization/rgi/main.nf | 4 ++-- .../nf-core/hamronization/summarize/main.nf | 6 +++--- tests/modules/nf-core/haplocheck/main.nf | 2 +- .../nf-core/haplogrep2/classify/main.nf | 2 +- tests/modules/nf-core/happy/happy/main.nf | 2 +- tests/modules/nf-core/happy/prepy/main.nf | 2 +- tests/modules/nf-core/hicap/main.nf | 2 +- tests/modules/nf-core/hifiasm/main.nf | 2 +- tests/modules/nf-core/hisat2/align/main.nf | 6 +++--- .../modules/nf-core/hisat2/build_test/main.nf | 4 ++-- .../nf-core/hisat2/extractsplicesites/main.nf | 2 +- .../modules/nf-core/hmmcopy/gccounter/main.nf | 2 +- .../nf-core/hmmcopy/generatemap/main.nf | 2 +- .../modules/nf-core/hmmcopy/mapcounter/main.nf | 4 ++-- .../nf-core/hmmcopy/readcounter/main.nf | 2 +- tests/modules/nf-core/hmmer/eslalimask/main.nf | 4 ++-- .../modules/nf-core/hmmer/eslreformat/main.nf | 8 ++++---- tests/modules/nf-core/hmmer/hmmalign/main.nf | 4 ++-- tests/modules/nf-core/hmmer/hmmbuild/main.nf | 2 +- tests/modules/nf-core/hmmer/hmmsearch/main.nf | 2 +- tests/modules/nf-core/hmtnote/main.nf | 2 +- .../nf-core/homer/annotatepeaks/main.nf | 2 +- tests/modules/nf-core/homer/findpeaks/main.nf | 4 ++-- .../nf-core/homer/maketagdirectory/main.nf | 2 +- .../modules/nf-core/homer/makeucscfile/main.nf | 4 ++-- tests/modules/nf-core/homer/pos2bed/main.nf | 6 +++--- tests/modules/nf-core/hpsuissero/main.nf | 2 +- .../modules/nf-core/ichorcna/createpon/main.nf | 2 +- tests/modules/nf-core/ichorcna/run/main.nf | 10 +++++----- tests/modules/nf-core/idr/main.nf | 2 +- .../modules/nf-core/imputeme/vcftoprs/main.nf | 2 +- tests/modules/nf-core/instrain/profile/main.nf | 2 +- tests/modules/nf-core/iqtree/main.nf | 2 +- tests/modules/nf-core/ismapper/main.nf | 2 +- tests/modules/nf-core/isoseq3/cluster/main.nf | 2 +- tests/modules/nf-core/isoseq3/refine/main.nf | 2 +- tests/modules/nf-core/ivar/consensus/main.nf | 2 +- tests/modules/nf-core/ivar/trim/main.nf | 2 +- tests/modules/nf-core/ivar/variants/main.nf | 2 +- tests/modules/nf-core/jupyternotebook/main.nf | 6 +++--- tests/modules/nf-core/kaiju/kaiju/main.nf | 4 ++-- .../modules/nf-core/kaiju/kaiju2krona/main.nf | 6 +++--- .../modules/nf-core/kaiju/kaiju2table/main.nf | 6 +++--- tests/modules/nf-core/kallisto/index/main.nf | 2 +- .../nf-core/kallistobustools/count/main.nf | 4 ++-- .../nf-core/kallistobustools/ref/main.nf | 2 +- tests/modules/nf-core/kat/hist/main.nf | 2 +- .../nf-core/khmer/normalizebymedian/main.nf | 6 +++--- .../modules/nf-core/khmer/uniquekmers/main.nf | 2 +- tests/modules/nf-core/kleborate/main.nf | 2 +- tests/modules/nf-core/kraken2/kraken2/main.nf | 4 ++-- .../krakentools/combinekreports/main.nf | 6 +++--- .../nf-core/krakentools/kreport2krona/main.nf | 6 +++--- tests/modules/nf-core/krona/kronadb/main.nf | 2 +- .../nf-core/krona/ktimporttaxonomy/main.nf | 4 ++-- .../modules/nf-core/krona/ktimporttext/main.nf | 2 +- .../nf-core/krona/ktupdatetaxonomy/main.nf | 2 +- tests/modules/nf-core/last/dotplot/main.nf | 2 +- tests/modules/nf-core/last/lastal/main.nf | 4 ++-- tests/modules/nf-core/last/lastdb/main.nf | 2 +- tests/modules/nf-core/last/mafconvert/main.nf | 2 +- tests/modules/nf-core/last/mafswap/main.nf | 2 +- tests/modules/nf-core/last/postmask/main.nf | 2 +- tests/modules/nf-core/last/split/main.nf | 2 +- tests/modules/nf-core/last/train/main.nf | 4 ++-- tests/modules/nf-core/leehom/main.nf | 4 ++-- tests/modules/nf-core/legsta/main.nf | 2 +- tests/modules/nf-core/lima/main.nf | 2 +- tests/modules/nf-core/lissero/main.nf | 2 +- tests/modules/nf-core/lofreq/call/main.nf | 2 +- .../nf-core/lofreq/callparallel/main.nf | 2 +- tests/modules/nf-core/lofreq/filter/main.nf | 2 +- tests/modules/nf-core/lofreq/indelqual/main.nf | 2 +- tests/modules/nf-core/macrel/contigs/main.nf | 2 +- tests/modules/nf-core/macs2/callpeak/main.nf | 6 +++--- tests/modules/nf-core/mafft/main.nf | 2 +- tests/modules/nf-core/malt/build_test/main.nf | 4 ++-- tests/modules/nf-core/malt/run/main.nf | 6 +++--- tests/modules/nf-core/maltextract/main.nf | 10 +++++----- .../nf-core/manta/convertinversion/main.nf | 4 ++-- tests/modules/nf-core/manta/germline/main.nf | 2 +- tests/modules/nf-core/manta/somatic/main.nf | 2 +- tests/modules/nf-core/manta/tumoronly/main.nf | 2 +- tests/modules/nf-core/mapdamage2/main.nf | 2 +- tests/modules/nf-core/mash/dist/main.nf | 2 +- tests/modules/nf-core/mash/screen/main.nf | 4 ++-- tests/modules/nf-core/mash/sketch/main.nf | 2 +- tests/modules/nf-core/mashtree/main.nf | 2 +- tests/modules/nf-core/maxbin2/main.nf | 2 +- tests/modules/nf-core/maxquant/lfq/main.nf | 2 +- tests/modules/nf-core/mcroni/main.nf | 2 +- tests/modules/nf-core/md5sum/main.nf | 2 +- tests/modules/nf-core/medaka/main.nf | 2 +- tests/modules/nf-core/megahit/main.nf | 2 +- tests/modules/nf-core/megan/daa2info/main.nf | 6 +++--- tests/modules/nf-core/megan/rma2info/main.nf | 2 +- tests/modules/nf-core/meningotype/main.nf | 2 +- tests/modules/nf-core/merqury/main.nf | 6 +++--- .../modules/nf-core/merquryfk/katcomp/main.nf | 6 +++--- tests/modules/nf-core/merquryfk/katgc/main.nf | 4 ++-- .../nf-core/merquryfk/merquryfk/main.nf | 4 ++-- .../nf-core/merquryfk/ploidyplot/main.nf | 4 ++-- tests/modules/nf-core/meryl/count/main.nf | 2 +- tests/modules/nf-core/meryl/histogram/main.nf | 4 ++-- tests/modules/nf-core/meryl/unionsum/main.nf | 4 ++-- .../jgisummarizebamcontigdepths/main.nf | 2 +- .../modules/nf-core/metabat2/metabat2/main.nf | 4 ++-- .../metaphlan3/mergemetaphlantables/main.nf | 6 +++--- .../nf-core/metaphlan3/metaphlan3/main.nf | 4 ++-- .../nf-core/methyldackel/extract/main.nf | 2 +- .../modules/nf-core/methyldackel/mbias/main.nf | 2 +- tests/modules/nf-core/minia/main.nf | 2 +- tests/modules/nf-core/miniasm/main.nf | 2 +- tests/modules/nf-core/minimap2/align/main.nf | 2 +- tests/modules/nf-core/minimap2/index/main.nf | 2 +- tests/modules/nf-core/mlst/main.nf | 2 +- tests/modules/nf-core/mobsuite/recon/main.nf | 2 +- tests/modules/nf-core/mosdepth/main.nf | 10 +++++----- tests/modules/nf-core/motus/downloaddb/main.nf | 2 +- tests/modules/nf-core/motus/merge/main.nf | 8 ++++---- tests/modules/nf-core/motus/profile/main.nf | 4 ++-- tests/modules/nf-core/msisensor/msi/main.nf | 4 ++-- tests/modules/nf-core/msisensor/scan/main.nf | 2 +- tests/modules/nf-core/msisensor2/msi/main.nf | 4 ++-- tests/modules/nf-core/msisensor2/scan/main.nf | 2 +- .../nf-core/msisensorpro/msi_somatic/main.nf | 4 ++-- .../modules/nf-core/msisensorpro/scan/main.nf | 2 +- tests/modules/nf-core/mtnucratio/main.nf | 2 +- tests/modules/nf-core/multiqc/main.nf | 6 +++--- tests/modules/nf-core/multivcfanalyzer/main.nf | 6 +++--- tests/modules/nf-core/mummer/main.nf | 2 +- tests/modules/nf-core/muscle/main.nf | 4 ++-- tests/modules/nf-core/mykrobe/predict/main.nf | 2 +- tests/modules/nf-core/nanolyse/main.nf | 2 +- tests/modules/nf-core/nanoplot/main.nf | 2 +- .../modules/nf-core/ncbigenomedownload/main.nf | 2 +- .../nf-core/nextclade/datasetget/main.nf | 2 +- tests/modules/nf-core/nextclade/run/main.nf | 4 ++-- tests/modules/nf-core/nextgenmap/main.nf | 2 +- tests/modules/nf-core/ngmaster/main.nf | 2 +- tests/modules/nf-core/ngscheckmate/ncm/main.nf | 10 +++++----- tests/modules/nf-core/nucmer/main.nf | 2 +- tests/modules/nf-core/optitype/main.nf | 2 +- tests/modules/nf-core/pairix/main.nf | 2 +- tests/modules/nf-core/pairtools/dedup/main.nf | 2 +- tests/modules/nf-core/pairtools/flip/main.nf | 2 +- tests/modules/nf-core/pairtools/parse/main.nf | 2 +- .../modules/nf-core/pairtools/restrict/main.nf | 2 +- tests/modules/nf-core/pairtools/select/main.nf | 2 +- tests/modules/nf-core/pairtools/sort/main.nf | 2 +- tests/modules/nf-core/panaroo/run/main.nf | 2 +- tests/modules/nf-core/pangolin/main.nf | 2 +- tests/modules/nf-core/paraclu/main.nf | 2 +- tests/modules/nf-core/pasty/main.nf | 2 +- tests/modules/nf-core/pbbam/pbmerge/main.nf | 2 +- tests/modules/nf-core/pbccs/main.nf | 2 +- tests/modules/nf-core/pbptyper/main.nf | 2 +- tests/modules/nf-core/pear/main.nf | 2 +- tests/modules/nf-core/peddy/main.nf | 2 +- .../nf-core/phantompeakqualtools/main.nf | 2 +- tests/modules/nf-core/phyloflash/main.nf | 2 +- .../picard/addorreplacereadgroups/main.nf | 2 +- tests/modules/nf-core/picard/cleansam/main.nf | 2 +- .../nf-core/picard/collecthsmetrics/main.nf | 2 +- .../picard/collectmultiplemetrics/main.nf | 2 +- .../nf-core/picard/collectwgsmetrics/main.nf | 2 +- .../picard/createsequencedictionary/main.nf | 2 +- .../picard/crosscheckfingerprints/main.nf | 2 +- .../modules/nf-core/picard/fastqtosam/main.nf | 2 +- .../nf-core/picard/filtersamreads/main.nf | 4 ++-- .../nf-core/picard/fixmateinformation/main.nf | 2 +- .../modules/nf-core/picard/liftovervcf/main.nf | 2 +- .../nf-core/picard/markduplicates/main.nf | 4 ++-- .../nf-core/picard/mergesamfiles/main.nf | 2 +- tests/modules/nf-core/picard/sortsam/main.nf | 2 +- tests/modules/nf-core/picard/sortvcf/main.nf | 2 +- tests/modules/nf-core/pints/caller/main.nf | 2 +- tests/modules/nf-core/pirate/main.nf | 2 +- tests/modules/nf-core/plasmidfinder/main.nf | 2 +- tests/modules/nf-core/plasmidid/main.nf | 2 +- tests/modules/nf-core/plink/extract/main.nf | 4 ++-- tests/modules/nf-core/plink/vcf/main.nf | 2 +- tests/modules/nf-core/plink2/extract/main.nf | 4 ++-- tests/modules/nf-core/plink2/score/main.nf | 4 ++-- tests/modules/nf-core/plink2/vcf/main.nf | 2 +- tests/modules/nf-core/pmdtools/filter/main.nf | 2 +- tests/modules/nf-core/porechop/main.nf | 2 +- tests/modules/nf-core/preseq/ccurve/main.nf | 2 +- tests/modules/nf-core/preseq/lcextrap/main.nf | 2 +- tests/modules/nf-core/prinseqplusplus/main.nf | 2 +- tests/modules/nf-core/prodigal/main.nf | 2 +- tests/modules/nf-core/prokka/main.nf | 2 +- tests/modules/nf-core/pycoqc/main.nf | 2 +- tests/modules/nf-core/pydamage/analyze/main.nf | 2 +- tests/modules/nf-core/pydamage/filter/main.nf | 4 ++-- tests/modules/nf-core/qcat/main.nf | 2 +- tests/modules/nf-core/qualimap/bamqc/main.nf | 2 +- .../modules/nf-core/qualimap/bamqccram/main.nf | 2 +- tests/modules/nf-core/quast/main.nf | 2 +- tests/modules/nf-core/racon/main.nf | 2 +- tests/modules/nf-core/rapidnj/main.nf | 2 +- tests/modules/nf-core/rasusa/main.nf | 2 +- tests/modules/nf-core/raven/main.nf | 2 +- tests/modules/nf-core/raxmlng/main.nf | 4 ++-- tests/modules/nf-core/rgi/main/main.nf | 2 +- tests/modules/nf-core/rhocall/annotate/main.nf | 4 ++-- .../modules/nf-core/rmarkdownnotebook/main.nf | 4 ++-- tests/modules/nf-core/roary/main.nf | 2 +- .../nf-core/rsem/calculateexpression/main.nf | 4 ++-- .../nf-core/rsem/preparereference/main.nf | 2 +- tests/modules/nf-core/rseqc/bamstat/main.nf | 2 +- .../nf-core/rseqc/inferexperiment/main.nf | 2 +- .../nf-core/rseqc/innerdistance/main.nf | 2 +- .../nf-core/rseqc/junctionannotation/main.nf | 2 +- .../nf-core/rseqc/junctionsaturation/main.nf | 2 +- .../nf-core/rseqc/readdistribution/main.nf | 2 +- .../nf-core/rseqc/readduplication/main.nf | 2 +- tests/modules/nf-core/rseqc/tin/main.nf | 2 +- .../modules/nf-core/rtgtools/pedfilter/main.nf | 2 +- tests/modules/nf-core/rtgtools/vcfeval/main.nf | 4 ++-- tests/modules/nf-core/salmon/index/main.nf | 2 +- tests/modules/nf-core/salmon/quant/main.nf | 4 ++-- tests/modules/nf-core/samblaster/main.nf | 2 +- .../nf-core/samtools/ampliconclip/main.nf | 2 +- tests/modules/nf-core/samtools/bam2fq/main.nf | 2 +- tests/modules/nf-core/samtools/collate/main.nf | 2 +- .../nf-core/samtools/collatefastq/main.nf | 2 +- tests/modules/nf-core/samtools/convert/main.nf | 4 ++-- tests/modules/nf-core/samtools/depth/main.nf | 2 +- tests/modules/nf-core/samtools/dict/main.nf | 2 +- tests/modules/nf-core/samtools/faidx/main.nf | 2 +- tests/modules/nf-core/samtools/fasta/main.nf | 2 +- tests/modules/nf-core/samtools/fastq/main.nf | 2 +- tests/modules/nf-core/samtools/fixmate/main.nf | 2 +- .../modules/nf-core/samtools/flagstat/main.nf | 2 +- tests/modules/nf-core/samtools/getrg/main.nf | 2 +- .../modules/nf-core/samtools/idxstats/main.nf | 2 +- tests/modules/nf-core/samtools/index/main.nf | 6 +++--- tests/modules/nf-core/samtools/markdup/main.nf | 8 ++++---- tests/modules/nf-core/samtools/merge/main.nf | 2 +- tests/modules/nf-core/samtools/mpileup/main.nf | 2 +- tests/modules/nf-core/samtools/sort/main.nf | 2 +- tests/modules/nf-core/samtools/stats/main.nf | 2 +- tests/modules/nf-core/samtools/view/main.nf | 2 +- tests/modules/nf-core/scoary/main.nf | 2 +- .../nf-core/scramble/clusteranalysis/main.nf | 4 ++-- .../nf-core/scramble/clusteridentifier/main.nf | 2 +- tests/modules/nf-core/seacr/callpeak/main.nf | 2 +- tests/modules/nf-core/seqkit/pair/main.nf | 2 +- tests/modules/nf-core/seqkit/replace/main.nf | 4 ++-- tests/modules/nf-core/seqkit/split2/main.nf | 6 +++--- tests/modules/nf-core/seqkit/stats/main.nf | 2 +- tests/modules/nf-core/seqsero2/main.nf | 2 +- tests/modules/nf-core/seqtk/mergepe/main.nf | 2 +- tests/modules/nf-core/seqtk/rename/main.nf | 2 +- tests/modules/nf-core/seqtk/sample/main.nf | 2 +- tests/modules/nf-core/seqtk/seq/main.nf | 2 +- tests/modules/nf-core/seqtk/subseq/main.nf | 2 +- .../nf-core/sequenzautils/bam2seqz/main.nf | 2 +- .../nf-core/sequenzautils/gcwiggle/main.nf | 2 +- tests/modules/nf-core/seqwish/induce/main.nf | 2 +- tests/modules/nf-core/seroba/run/main.nf | 2 +- tests/modules/nf-core/sexdeterrmine/main.nf | 4 ++-- tests/modules/nf-core/shasta/main.nf | 2 +- tests/modules/nf-core/shasum/main.nf | 2 +- tests/modules/nf-core/shigatyper/main.nf | 2 +- tests/modules/nf-core/shovill/main.nf | 8 ++++---- tests/modules/nf-core/sistr/main.nf | 2 +- tests/modules/nf-core/slimfastq/main.nf | 2 +- .../modules/nf-core/snapaligner/align/main.nf | 4 ++-- .../modules/nf-core/snapaligner/index/main.nf | 2 +- tests/modules/nf-core/snippy/core/main.nf | 4 ++-- tests/modules/nf-core/snippy/run/main.nf | 2 +- tests/modules/nf-core/snpdists/main.nf | 2 +- tests/modules/nf-core/snpeff/main.nf | 2 +- tests/modules/nf-core/snpsift/split/main.nf | 2 +- tests/modules/nf-core/snpsites/main.nf | 2 +- tests/modules/nf-core/somalier/extract/main.nf | 2 +- tests/modules/nf-core/somalier/relate/main.nf | 2 +- tests/modules/nf-core/sourmash/sketch/main.nf | 2 +- tests/modules/nf-core/spades/main.nf | 2 +- tests/modules/nf-core/spatyper/main.nf | 4 ++-- .../nf-core/sratools/fasterqdump/main.nf | 4 ++-- .../modules/nf-core/sratools/prefetch/main.nf | 2 +- tests/modules/nf-core/srst2/srst2/main.nf | 2 +- tests/modules/nf-core/ssuissero/main.nf | 2 +- .../nf-core/stadeniolib/scramble/main.nf | 2 +- tests/modules/nf-core/staphopiasccmec/main.nf | 4 ++-- tests/modules/nf-core/star/align/main.nf | 8 ++++---- .../nf-core/star/genomegenerate/main.nf | 2 +- tests/modules/nf-core/stranger/main.nf | 4 ++-- tests/modules/nf-core/strelka/germline/main.nf | 2 +- tests/modules/nf-core/strelka/somatic/main.nf | 2 +- tests/modules/nf-core/stringtie/merge/main.nf | 4 ++-- .../nf-core/stringtie/stringtie/main.nf | 2 +- .../nf-core/subread/featurecounts/main.nf | 2 +- tests/modules/nf-core/svdb/merge/main.nf | 2 +- tests/modules/nf-core/svdb/query/main.nf | 2 +- tests/modules/nf-core/svtk/standardize/main.nf | 4 ++-- tests/modules/nf-core/tabix/bgzip/main.nf | 4 ++-- tests/modules/nf-core/tabix/bgziptabix/main.nf | 2 +- tests/modules/nf-core/tabix/tabix/main.nf | 8 ++++---- tests/modules/nf-core/tailfindr/main.nf | 2 +- .../modules/nf-core/tbprofiler/profile/main.nf | 2 +- tests/modules/nf-core/tiddit/cov/main.nf | 4 ++-- tests/modules/nf-core/tiddit/sv/main.nf | 6 +++--- .../nf-core/transdecoder/longorf/main.nf | 2 +- .../nf-core/transdecoder/predict/main.nf | 4 ++-- tests/modules/nf-core/trimgalore/main.nf | 2 +- tests/modules/nf-core/trimmomatic/main.nf | 2 +- tests/modules/nf-core/ucsc/bedclip/main.nf | 2 +- .../nf-core/ucsc/bedgraphtobigwig/main.nf | 2 +- tests/modules/nf-core/ucsc/bedtobigbed/main.nf | 4 ++-- .../nf-core/ucsc/bigwigaverageoverbed/main.nf | 2 +- tests/modules/nf-core/ucsc/liftover/main.nf | 2 +- tests/modules/nf-core/ucsc/wigtobigwig/main.nf | 2 +- tests/modules/nf-core/ultra/align/main.nf | 8 ++++---- tests/modules/nf-core/ultra/index/main.nf | 4 ++-- tests/modules/nf-core/ultra/pipeline/main.nf | 6 +++--- tests/modules/nf-core/umitools/dedup/main.nf | 10 +++++----- tests/modules/nf-core/umitools/extract/main.nf | 2 +- tests/modules/nf-core/unicycler/main.nf | 2 +- tests/modules/nf-core/untar/main.nf | 2 +- tests/modules/nf-core/unzip/main.nf | 2 +- tests/modules/nf-core/vardictjava/main.nf | 2 +- tests/modules/nf-core/variantbam/main.nf | 2 +- tests/modules/nf-core/vcf2db/main.nf | 2 +- tests/modules/nf-core/vcf2maf/main.nf | 4 ++-- tests/modules/nf-core/vcfanno/main.nf | 4 ++-- .../nf-core/vcflib/vcfbreakmulti/main.nf | 2 +- tests/modules/nf-core/vcflib/vcfuniq/main.nf | 2 +- tests/modules/nf-core/vcftools/main.nf | 4 ++-- tests/modules/nf-core/vsearch/sintax/main.nf | 2 +- .../nf-core/vsearch/usearchglobal/main.nf | 2 +- tests/modules/nf-core/whamg/main.nf | 2 +- tests/modules/nf-core/yara/index/main.nf | 2 +- tests/modules/nf-core/yara/mapper/main.nf | 4 ++-- 631 files changed, 968 insertions(+), 968 deletions(-) diff --git a/tests/modules/nf-core/abacas/main.nf b/tests/modules/nf-core/abacas/main.nf index 542a67af07d..7115c292d72 100644 --- a/tests/modules/nf-core/abacas/main.nf +++ b/tests/modules/nf-core/abacas/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ABACAS } from '../../../modules/abacas/main.nf' +include { ABACAS } from '../../../modules/nf-core/abacas/main.nf' workflow test_abacas { diff --git a/tests/modules/nf-core/abricate/run/main.nf b/tests/modules/nf-core/abricate/run/main.nf index 19d1f8a83e3..2f15aaba3b6 100644 --- a/tests/modules/nf-core/abricate/run/main.nf +++ b/tests/modules/nf-core/abricate/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ABRICATE_RUN } from '../../../../modules/abricate/run/main.nf' +include { ABRICATE_RUN } from '../../../../modules/nf-core/abricate/run/main.nf' workflow test_abricate_run { diff --git a/tests/modules/nf-core/abricate/summary/main.nf b/tests/modules/nf-core/abricate/summary/main.nf index 9acbdba9bc6..d6f92a6ad33 100644 --- a/tests/modules/nf-core/abricate/summary/main.nf +++ b/tests/modules/nf-core/abricate/summary/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ABRICATE_RUN } from '../../../../modules/abricate/run/main.nf' -include { ABRICATE_SUMMARY } from '../../../../modules/abricate/summary/main.nf' +include { ABRICATE_RUN } from '../../../../modules/nf-core/abricate/run/main.nf' +include { ABRICATE_SUMMARY } from '../../../../modules/nf-core/abricate/summary/main.nf' workflow test_abricate_summary { diff --git a/tests/modules/nf-core/adapterremoval/main.nf b/tests/modules/nf-core/adapterremoval/main.nf index a427bfbfc2c..b54c405fa2a 100644 --- a/tests/modules/nf-core/adapterremoval/main.nf +++ b/tests/modules/nf-core/adapterremoval/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf' -include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../modules/adapterremoval/main.nf' +include { ADAPTERREMOVAL } from '../../../modules/nf-core/adapterremoval/main.nf' +include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../modules/nf-core/adapterremoval/main.nf' workflow test_adapterremoval_single_end { diff --git a/tests/modules/nf-core/adapterremovalfixprefix/main.nf b/tests/modules/nf-core/adapterremovalfixprefix/main.nf index 863a7ca81db..10f4a3bebb8 100644 --- a/tests/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/tests/modules/nf-core/adapterremovalfixprefix/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf' -include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/adapterremovalfixprefix/main.nf' +include { ADAPTERREMOVAL } from '../../../modules/nf-core/adapterremoval/main.nf' +include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/nf-core/adapterremovalfixprefix/main.nf' workflow test_adapterremovalfixprefix { diff --git a/tests/modules/nf-core/agrvate/main.nf b/tests/modules/nf-core/agrvate/main.nf index ac682bef93f..069a800562c 100644 --- a/tests/modules/nf-core/agrvate/main.nf +++ b/tests/modules/nf-core/agrvate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { AGRVATE } from '../../../modules/agrvate/main.nf' +include { AGRVATE } from '../../../modules/nf-core/agrvate/main.nf' workflow test_agrvate { diff --git a/tests/modules/nf-core/allelecounter/main.nf b/tests/modules/nf-core/allelecounter/main.nf index 3fe11be3f30..380d7d9340a 100644 --- a/tests/modules/nf-core/allelecounter/main.nf +++ b/tests/modules/nf-core/allelecounter/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { ALLELECOUNTER } from '../../../modules/allelecounter/main.nf' +include { ALLELECOUNTER } from '../../../modules/nf-core/allelecounter/main.nf' workflow test_allelecounter_bam { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/ampir/main.nf b/tests/modules/nf-core/ampir/main.nf index bee2ff90631..76d4fda112f 100644 --- a/tests/modules/nf-core/ampir/main.nf +++ b/tests/modules/nf-core/ampir/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { AMPIR } from '../../../modules/ampir/main.nf' +include { AMPIR } from '../../../modules/nf-core/ampir/main.nf' workflow test_ampir { diff --git a/tests/modules/nf-core/amplify/predict/main.nf b/tests/modules/nf-core/amplify/predict/main.nf index 05db4cdbfdf..1c55561676d 100644 --- a/tests/modules/nf-core/amplify/predict/main.nf +++ b/tests/modules/nf-core/amplify/predict/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PRODIGAL } from '../../../modules/prodigal/main.nf' addParams( options: [:] ) -include { AMPLIFY_PREDICT } from '../../../../modules/amplify/predict/main.nf' addParams( options: [:] ) +include { PRODIGAL } from '../../../modules/nf-core/prodigal/main.nf' addParams( options: [:] ) +include { AMPLIFY_PREDICT } from '../../../../modules/nf-core/amplify/predict/main.nf' addParams( options: [:] ) workflow amplify_predict { diff --git a/tests/modules/nf-core/amps/main.nf b/tests/modules/nf-core/amps/main.nf index 7c4969e9bfe..53eeda2df03 100644 --- a/tests/modules/nf-core/amps/main.nf +++ b/tests/modules/nf-core/amps/main.nf @@ -2,12 +2,12 @@ nextflow.enable.dsl = 2 -include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf' -include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf' -include { MALT_BUILD } from '../../../modules/malt/build/main.nf' -include { MALT_RUN } from '../../../modules/malt/run/main.nf' -include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' -include { AMPS } from '../../../modules/amps/main.nf' +include { UNZIP as UNZIP_MALT } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../modules/nf-core/malt/build/main.nf' +include { MALT_RUN } from '../../../modules/nf-core/malt/run/main.nf' +include { MALTEXTRACT } from '../../../modules/nf-core/maltextract/main.nf' +include { AMPS } from '../../../modules/nf-core/amps/main.nf' workflow test_amps { diff --git a/tests/modules/nf-core/amrfinderplus/run/main.nf b/tests/modules/nf-core/amrfinderplus/run/main.nf index 917ac28d46c..8e807301b70 100644 --- a/tests/modules/nf-core/amrfinderplus/run/main.nf +++ b/tests/modules/nf-core/amrfinderplus/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { AMRFINDERPLUS_UPDATE } from '../../../../modules/amrfinderplus/update/main.nf' -include { AMRFINDERPLUS_RUN } from '../../../../modules/amrfinderplus/run/main.nf' +include { AMRFINDERPLUS_UPDATE } from '../../../../modules/nf-core/amrfinderplus/update/main.nf' +include { AMRFINDERPLUS_RUN } from '../../../../modules/nf-core/amrfinderplus/run/main.nf' workflow test_amrfinderplus_run { diff --git a/tests/modules/nf-core/amrfinderplus/update/main.nf b/tests/modules/nf-core/amrfinderplus/update/main.nf index f3a34ea0d72..08f4060f84f 100644 --- a/tests/modules/nf-core/amrfinderplus/update/main.nf +++ b/tests/modules/nf-core/amrfinderplus/update/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { AMRFINDERPLUS_UPDATE } from '../../../../modules/amrfinderplus/update/main.nf' +include { AMRFINDERPLUS_UPDATE } from '../../../../modules/nf-core/amrfinderplus/update/main.nf' workflow test_amrfinderplus_update { diff --git a/tests/modules/nf-core/angsd/docounts/main.nf b/tests/modules/nf-core/angsd/docounts/main.nf index 59e999f1a47..e6960bb8bac 100644 --- a/tests/modules/nf-core/angsd/docounts/main.nf +++ b/tests/modules/nf-core/angsd/docounts/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ANGSD_DOCOUNTS } from '../../../../modules/angsd/docounts/main.nf' +include { ANGSD_DOCOUNTS } from '../../../../modules/nf-core/angsd/docounts/main.nf' workflow test_angsd_docounts { diff --git a/tests/modules/nf-core/antismash/antismashlite/main.nf b/tests/modules/nf-core/antismash/antismashlite/main.nf index 2b23c400ff2..258654fcedd 100644 --- a/tests/modules/nf-core/antismash/antismashlite/main.nf +++ b/tests/modules/nf-core/antismash/antismashlite/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf' -include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf' -include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf' -include { GUNZIP as GUNZIP2 } from '../../../../modules/gunzip/main.nf' -include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf' -include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf' -include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf' +include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/nf-core/antismash/antismashlite/main.nf' +include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf' +include { GUNZIP as GUNZIP1 } from '../../../../modules/nf-core/gunzip/main.nf' +include { GUNZIP as GUNZIP2 } from '../../../../modules/nf-core/gunzip/main.nf' +include { UNTAR as UNTAR1 } from '../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR2 } from '../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR3 } from '../../../../modules/nf-core/untar/main.nf' workflow test_antismashlite { genome_fna = [ diff --git a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index d7289acc0c7..5faf2111639 100644 --- a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf' -include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf' -include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf' -include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/antismash/antismashlitedownloaddatabases/main.nf' +include { UNTAR as UNTAR1 } from '../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR2 } from '../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR3 } from '../../../../modules/nf-core/untar/main.nf' +include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf' workflow test_antismash_antismashlitedownloaddatabases { input1 = [ diff --git a/tests/modules/nf-core/ariba/getref/main.nf b/tests/modules/nf-core/ariba/getref/main.nf index 8af67f74450..f5d32fc0cd1 100644 --- a/tests/modules/nf-core/ariba/getref/main.nf +++ b/tests/modules/nf-core/ariba/getref/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ARIBA_GETREF } from '../../../../modules/ariba/getref/main.nf' +include { ARIBA_GETREF } from '../../../../modules/nf-core/ariba/getref/main.nf' workflow test_ariba_getref { ARIBA_GETREF ( "card" ) diff --git a/tests/modules/nf-core/ariba/run/main.nf b/tests/modules/nf-core/ariba/run/main.nf index 02244d9d4ae..eea3cd12b62 100644 --- a/tests/modules/nf-core/ariba/run/main.nf +++ b/tests/modules/nf-core/ariba/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ARIBA_GETREF } from '../../../../modules/ariba/getref/main.nf' -include { ARIBA_RUN } from '../../../../modules/ariba/run/main.nf' +include { ARIBA_GETREF } from '../../../../modules/nf-core/ariba/getref/main.nf' +include { ARIBA_RUN } from '../../../../modules/nf-core/ariba/run/main.nf' workflow test_ariba_run { diff --git a/tests/modules/nf-core/arriba/main.nf b/tests/modules/nf-core/arriba/main.nf index 205adf0f3c0..c0072d1da3c 100644 --- a/tests/modules/nf-core/arriba/main.nf +++ b/tests/modules/nf-core/arriba/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../modules/star/genomegenerate/main.nf' -include { STAR_ALIGN } from '../../../modules/star/align/main.nf' -include { ARRIBA } from '../../../modules/arriba/main.nf' +include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main.nf' +include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main.nf' +include { ARRIBA } from '../../../modules/nf-core/arriba/main.nf' workflow test_arriba_single_end { diff --git a/tests/modules/nf-core/artic/guppyplex/main.nf b/tests/modules/nf-core/artic/guppyplex/main.nf index 89f67c746ee..83821e4212a 100644 --- a/tests/modules/nf-core/artic/guppyplex/main.nf +++ b/tests/modules/nf-core/artic/guppyplex/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ARTIC_GUPPYPLEX } from '../../../../modules/artic/guppyplex/main.nf' +include { ARTIC_GUPPYPLEX } from '../../../../modules/nf-core/artic/guppyplex/main.nf' process STAGE_FASTQ_DIR { input: diff --git a/tests/modules/nf-core/artic/minion/main.nf b/tests/modules/nf-core/artic/minion/main.nf index b70b549e3f0..4badfa5d597 100644 --- a/tests/modules/nf-core/artic/minion/main.nf +++ b/tests/modules/nf-core/artic/minion/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { ARTIC_MINION } from '../../../../modules/nf-core/artic/minion/main.nf' workflow test_artic_minion { diff --git a/tests/modules/nf-core/ascat/main.nf b/tests/modules/nf-core/ascat/main.nf index 83b5eeb84b6..c2efec3bb14 100644 --- a/tests/modules/nf-core/ascat/main.nf +++ b/tests/modules/nf-core/ascat/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { ASCAT as ASCAT_SIMPLE } from '../../../modules/ascat/main.nf' -include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../modules/ascat/main.nf' -include { ASCAT as ASCAT_CRAM } from '../../../modules/ascat/main.nf' -include { UNZIP as UNZIP_ALLELES } from '../../../modules/unzip/main.nf' -include { UNZIP as UNZIP_LOCI } from '../../../modules/unzip/main.nf' -include { UNZIP as UNZIP_GC } from '../../../modules/unzip/main.nf' -include { UNZIP as UNZIP_RT } from '../../../modules/unzip/main.nf' +include { ASCAT as ASCAT_SIMPLE } from '../../../modules/nf-core/ascat/main.nf' +include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../modules/nf-core/ascat/main.nf' +include { ASCAT as ASCAT_CRAM } from '../../../modules/nf-core/ascat/main.nf' +include { UNZIP as UNZIP_ALLELES } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_LOCI } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_GC } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_RT } from '../../../modules/nf-core/unzip/main.nf' diff --git a/tests/modules/nf-core/assemblyscan/main.nf b/tests/modules/nf-core/assemblyscan/main.nf index 7cd5f3932a1..b1fbf954c54 100644 --- a/tests/modules/nf-core/assemblyscan/main.nf +++ b/tests/modules/nf-core/assemblyscan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ASSEMBLYSCAN } from '../../../modules/assemblyscan/main.nf' +include { ASSEMBLYSCAN } from '../../../modules/nf-core/assemblyscan/main.nf' workflow test_assemblyscan { diff --git a/tests/modules/nf-core/ataqv/ataqv/main.nf b/tests/modules/nf-core/ataqv/ataqv/main.nf index b1103350e8a..a11859df647 100644 --- a/tests/modules/nf-core/ataqv/ataqv/main.nf +++ b/tests/modules/nf-core/ataqv/ataqv/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf' -include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../modules/ataqv/ataqv/main.nf' +include { ATAQV_ATAQV } from '../../../../modules/nf-core/ataqv/ataqv/main.nf' +include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../modules/nf-core/ataqv/ataqv/main.nf' workflow test_ataqv_ataqv { diff --git a/tests/modules/nf-core/ataqv/mkarv/main.nf b/tests/modules/nf-core/ataqv/mkarv/main.nf index d5bab5c5c69..003cb34e06a 100644 --- a/tests/modules/nf-core/ataqv/mkarv/main.nf +++ b/tests/modules/nf-core/ataqv/mkarv/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf' -include { ATAQV_MKARV } from '../../../../modules/ataqv/mkarv/main.nf' +include { ATAQV_ATAQV } from '../../../../modules/nf-core/ataqv/ataqv/main.nf' +include { ATAQV_MKARV } from '../../../../modules/nf-core/ataqv/mkarv/main.nf' workflow test_ataqv_mkarv { diff --git a/tests/modules/nf-core/atlas/call/main.nf b/tests/modules/nf-core/atlas/call/main.nf index 945812ef395..ed01849d9cf 100644 --- a/tests/modules/nf-core/atlas/call/main.nf +++ b/tests/modules/nf-core/atlas/call/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_CALL } from '../../../../modules/atlas/call/main.nf' +include { ATLAS_CALL } from '../../../../modules/nf-core/atlas/call/main.nf' workflow test_atlas_call { diff --git a/tests/modules/nf-core/atlas/pmd/main.nf b/tests/modules/nf-core/atlas/pmd/main.nf index db552f8d7dc..26d8d2e5fb1 100644 --- a/tests/modules/nf-core/atlas/pmd/main.nf +++ b/tests/modules/nf-core/atlas/pmd/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_PMD } from '../../../../modules/atlas/pmd/main.nf' +include { ATLAS_PMD } from '../../../../modules/nf-core/atlas/pmd/main.nf' workflow test_atlas_pmd { diff --git a/tests/modules/nf-core/atlas/recal/main.nf b/tests/modules/nf-core/atlas/recal/main.nf index d74fa55a907..df69f99873d 100644 --- a/tests/modules/nf-core/atlas/recal/main.nf +++ b/tests/modules/nf-core/atlas/recal/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_RECAL } from '../../../../modules/atlas/recal/main.nf' +include { ATLAS_RECAL } from '../../../../modules/nf-core/atlas/recal/main.nf' workflow test_atlas_recal { diff --git a/tests/modules/nf-core/atlas/splitmerge/main.nf b/tests/modules/nf-core/atlas/splitmerge/main.nf index 9334c27f60b..10f6058ce76 100644 --- a/tests/modules/nf-core/atlas/splitmerge/main.nf +++ b/tests/modules/nf-core/atlas/splitmerge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_SPLITMERGE } from '../../../../modules/atlas/splitmerge/main.nf' +include { ATLAS_SPLITMERGE } from '../../../../modules/nf-core/atlas/splitmerge/main.nf' //MAIN workflow test_atlas_splitmerge { diff --git a/tests/modules/nf-core/bakta/main.nf b/tests/modules/nf-core/bakta/main.nf index 1bc0062237b..c9221b6b7a2 100644 --- a/tests/modules/nf-core/bakta/main.nf +++ b/tests/modules/nf-core/bakta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAKTA } from '../../../modules/bakta/main.nf' +include { BAKTA } from '../../../modules/nf-core/bakta/main.nf' workflow test_bakta { diff --git a/tests/modules/nf-core/bamaligncleaner/main.nf b/tests/modules/nf-core/bamaligncleaner/main.nf index c9d517ae0fe..b7072779a79 100644 --- a/tests/modules/nf-core/bamaligncleaner/main.nf +++ b/tests/modules/nf-core/bamaligncleaner/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAMALIGNCLEANER } from '../../../modules/bamaligncleaner/main.nf' +include { BAMALIGNCLEANER } from '../../../modules/nf-core/bamaligncleaner/main.nf' workflow test_bamaligncleaner { diff --git a/tests/modules/nf-core/bamcmp/main.nf b/tests/modules/nf-core/bamcmp/main.nf index cf7964063f0..279dd92d063 100644 --- a/tests/modules/nf-core/bamcmp/main.nf +++ b/tests/modules/nf-core/bamcmp/main.nf @@ -2,15 +2,15 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../modules/bwa/index/main.nf' -include { BWA_MEM } from '../../../modules/bwa/mem/main.nf' -include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../modules/bwa/index/main.nf' -include { BWA_MEM as BWA_MEM_COV2 } from '../../../modules/bwa/mem/main.nf' +include { BWA_INDEX } from '../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM } from '../../../modules/nf-core/bwa/mem/main.nf' +include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM as BWA_MEM_COV2 } from '../../../modules/nf-core/bwa/mem/main.nf' -include { SAMTOOLS_SORT } from '../../../modules/samtools/sort/main.nf' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2 } from '../../../modules/samtools/sort/main.nf' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main.nf' +include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2 } from '../../../modules/nf-core/samtools/sort/main.nf' -include { BAMCMP } from '../../../modules/bamcmp/main.nf' +include { BAMCMP } from '../../../modules/nf-core/bamcmp/main.nf' workflow test_bamcmp { diff --git a/tests/modules/nf-core/bamtools/convert/main.nf b/tests/modules/nf-core/bamtools/convert/main.nf index bf57f2489db..f719f615969 100644 --- a/tests/modules/nf-core/bamtools/convert/main.nf +++ b/tests/modules/nf-core/bamtools/convert/main.nf @@ -2,15 +2,15 @@ nextflow.enable.dsl = 2 -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/nf-core/bamtools/convert/main.nf' workflow test_bamtools_convert_ext_error { diff --git a/tests/modules/nf-core/bamtools/split/main.nf b/tests/modules/nf-core/bamtools/split/main.nf index e5c15c3202d..ea0e46ef51a 100644 --- a/tests/modules/nf-core/bamtools/split/main.nf +++ b/tests/modules/nf-core/bamtools/split/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE } from '../../../../modules/bamtools/split/main.nf' -include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf' +include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE } from '../../../../modules/nf-core/bamtools/split/main.nf' +include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/nf-core/bamtools/split/main.nf' workflow test_bamtools_split_single_input { diff --git a/tests/modules/nf-core/bamtools/stats/main.nf b/tests/modules/nf-core/bamtools/stats/main.nf index e5fd3953116..38aea055e49 100644 --- a/tests/modules/nf-core/bamtools/stats/main.nf +++ b/tests/modules/nf-core/bamtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAMTOOLS_STATS } from '../../../../modules/bamtools/stats/main.nf' +include { BAMTOOLS_STATS } from '../../../../modules/nf-core/bamtools/stats/main.nf' workflow test_bamtools_stats { diff --git a/tests/modules/nf-core/bamutil/trimbam/main.nf b/tests/modules/nf-core/bamutil/trimbam/main.nf index 2967b038f67..659e9d7d6bf 100644 --- a/tests/modules/nf-core/bamutil/trimbam/main.nf +++ b/tests/modules/nf-core/bamutil/trimbam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAMUTIL_TRIMBAM } from '../../../../modules/bamutil/trimbam/main.nf' +include { BAMUTIL_TRIMBAM } from '../../../../modules/nf-core/bamutil/trimbam/main.nf' workflow test_bamutil_trimbam { diff --git a/tests/modules/nf-core/bandage/image/main.nf b/tests/modules/nf-core/bandage/image/main.nf index 15f01ab16bb..a5eea45be03 100644 --- a/tests/modules/nf-core/bandage/image/main.nf +++ b/tests/modules/nf-core/bandage/image/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BANDAGE_IMAGE } from '../../../../modules/bandage/image/main.nf' +include { BANDAGE_IMAGE } from '../../../../modules/nf-core/bandage/image/main.nf' workflow test_bandage_image { input = [ diff --git a/tests/modules/nf-core/bases2fastq/main.nf b/tests/modules/nf-core/bases2fastq/main.nf index abd1f92b613..af6b8e3e419 100644 --- a/tests/modules/nf-core/bases2fastq/main.nf +++ b/tests/modules/nf-core/bases2fastq/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BASES2FASTQ } from '../../../modules/bases2fastq/main.nf' -include { UNTAR } from '../../../modules/untar/main.nf' +include { BASES2FASTQ } from '../../../modules/nf-core/bases2fastq/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' workflow test_bases2fastq { diff --git a/tests/modules/nf-core/bbmap/align/main.nf b/tests/modules/nf-core/bbmap/align/main.nf index c7a02e2a502..8e816212fd1 100644 --- a/tests/modules/nf-core/bbmap/align/main.nf +++ b/tests/modules/nf-core/bbmap/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' -include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf' -include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf' +include { BBMAP_INDEX } from '../../../../modules/nf-core/bbmap/index/main.nf' +include { BBMAP_ALIGN } from '../../../../modules/nf-core/bbmap/align/main.nf' +include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/nf-core/bbmap/align/main.nf' workflow test_bbmap_align_paired_end_fasta_ref { diff --git a/tests/modules/nf-core/bbmap/bbduk/main.nf b/tests/modules/nf-core/bbmap/bbduk/main.nf index e1f0c2dee67..452dae2adcc 100644 --- a/tests/modules/nf-core/bbmap/bbduk/main.nf +++ b/tests/modules/nf-core/bbmap/bbduk/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_BBDUK } from '../../../../modules/bbmap/bbduk/main.nf' +include { BBMAP_BBDUK } from '../../../../modules/nf-core/bbmap/bbduk/main.nf' workflow test_bbmap_bbduk_single_end { diff --git a/tests/modules/nf-core/bbmap/bbsplit/main.nf b/tests/modules/nf-core/bbmap/bbsplit/main.nf index d12360618a6..7960dbe7e52 100644 --- a/tests/modules/nf-core/bbmap/bbsplit/main.nf +++ b/tests/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/bbmap/bbsplit/main.nf' -include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/bbmap/bbsplit/main.nf' +include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/nf-core/bbmap/bbsplit/main.nf' +include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/nf-core/bbmap/bbsplit/main.nf' workflow test_bbmap_bbsplit { diff --git a/tests/modules/nf-core/bbmap/clumpify/main.nf b/tests/modules/nf-core/bbmap/clumpify/main.nf index 54cbaadad90..77c776c5a44 100644 --- a/tests/modules/nf-core/bbmap/clumpify/main.nf +++ b/tests/modules/nf-core/bbmap/clumpify/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_CLUMPIFY } from '../../../../modules/bbmap/clumpify/main.nf' +include { BBMAP_CLUMPIFY } from '../../../../modules/nf-core/bbmap/clumpify/main.nf' workflow test_bbmap_clumpify_single_end { diff --git a/tests/modules/nf-core/bbmap/index/main.nf b/tests/modules/nf-core/bbmap/index/main.nf index a6f111f4308..811100e8fc3 100644 --- a/tests/modules/nf-core/bbmap/index/main.nf +++ b/tests/modules/nf-core/bbmap/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' +include { BBMAP_INDEX } from '../../../../modules/nf-core/bbmap/index/main.nf' workflow test_bbmap_index { diff --git a/tests/modules/nf-core/bbmap/pileup/main.nf b/tests/modules/nf-core/bbmap/pileup/main.nf index 943df9b5ba5..d63b8c426be 100644 --- a/tests/modules/nf-core/bbmap/pileup/main.nf +++ b/tests/modules/nf-core/bbmap/pileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_PILEUP } from '../../../../modules/bbmap/pileup/main.nf' +include { BBMAP_PILEUP } from '../../../../modules/nf-core/bbmap/pileup/main.nf' workflow test_bbmap_pileup { diff --git a/tests/modules/nf-core/bcftools/annotate/main.nf b/tests/modules/nf-core/bcftools/annotate/main.nf index 0d096ca996e..2b2a620a90b 100644 --- a/tests/modules/nf-core/bcftools/annotate/main.nf +++ b/tests/modules/nf-core/bcftools/annotate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf' +include { BCFTOOLS_ANNOTATE } from '../../../../modules/nf-core/bcftools/annotate/main.nf' workflow test_bcftools_annotate_out_vcf { diff --git a/tests/modules/nf-core/bcftools/concat/main.nf b/tests/modules/nf-core/bcftools/concat/main.nf index 777dc5b8ce0..3455f9a28e7 100644 --- a/tests/modules/nf-core/bcftools/concat/main.nf +++ b/tests/modules/nf-core/bcftools/concat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf' +include { BCFTOOLS_CONCAT } from '../../../../modules/nf-core/bcftools/concat/main.nf' workflow test_bcftools_concat_tbi { diff --git a/tests/modules/nf-core/bcftools/consensus/main.nf b/tests/modules/nf-core/bcftools/consensus/main.nf index b2ee899bbcb..431946ed4cd 100644 --- a/tests/modules/nf-core/bcftools/consensus/main.nf +++ b/tests/modules/nf-core/bcftools/consensus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONSENSUS } from '../../../../modules/bcftools/consensus/main.nf' +include { BCFTOOLS_CONSENSUS } from '../../../../modules/nf-core/bcftools/consensus/main.nf' workflow test_bcftools_consensus { diff --git a/tests/modules/nf-core/bcftools/convert/main.nf b/tests/modules/nf-core/bcftools/convert/main.nf index 9277b2d1251..f7e2276bb70 100644 --- a/tests/modules/nf-core/bcftools/convert/main.nf +++ b/tests/modules/nf-core/bcftools/convert/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../modules/bcftools/convert/main.nf' -include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF } from '../../../../modules/bcftools/convert/main.nf' +include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../modules/nf-core/bcftools/convert/main.nf' +include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF } from '../../../../modules/nf-core/bcftools/convert/main.nf' workflow test_bcftools_convert_gvcf { diff --git a/tests/modules/nf-core/bcftools/filter/main.nf b/tests/modules/nf-core/bcftools/filter/main.nf index 85fbf950e3a..bf1fb3b52d4 100644 --- a/tests/modules/nf-core/bcftools/filter/main.nf +++ b/tests/modules/nf-core/bcftools/filter/main.nf @@ -3,7 +3,7 @@ nextflow.enable.dsl = 2 //keep --no-verson argument, otherwise md5 will change on each execution -include { BCFTOOLS_FILTER } from '../../../../modules/bcftools/filter/main.nf' +include { BCFTOOLS_FILTER } from '../../../../modules/nf-core/bcftools/filter/main.nf' workflow test_bcftools_filter { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/index/main.nf b/tests/modules/nf-core/bcftools/index/main.nf index 839cd988c85..35228bcd608 100644 --- a/tests/modules/nf-core/bcftools/index/main.nf +++ b/tests/modules/nf-core/bcftools/index/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../modules/bcftools/index/main.nf' -include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../modules/bcftools/index/main.nf' +include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../modules/nf-core/bcftools/index/main.nf' +include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../modules/nf-core/bcftools/index/main.nf' workflow test_bcftools_index_csi { diff --git a/tests/modules/nf-core/bcftools/isec/main.nf b/tests/modules/nf-core/bcftools/isec/main.nf index 0b8ffc5cd0e..e75cc3dd15e 100644 --- a/tests/modules/nf-core/bcftools/isec/main.nf +++ b/tests/modules/nf-core/bcftools/isec/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_ISEC } from '../../../../modules/bcftools/isec/main.nf' +include { BCFTOOLS_ISEC } from '../../../../modules/nf-core/bcftools/isec/main.nf' workflow test_bcftools_isec { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/merge/main.nf b/tests/modules/nf-core/bcftools/merge/main.nf index 0ec188d2d96..7a0f10e813f 100644 --- a/tests/modules/nf-core/bcftools/merge/main.nf +++ b/tests/modules/nf-core/bcftools/merge/main.nf @@ -3,9 +3,9 @@ nextflow.enable.dsl = 2 //keep --no-verson argument, otherwise md5 will change on each execution -include { BCFTOOLS_MERGE } from '../../../../modules/bcftools/merge/main.nf' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../modules/bcftools/merge/main.nf' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF } from '../../../../modules/bcftools/merge/main.nf' +include { BCFTOOLS_MERGE } from '../../../../modules/nf-core/bcftools/merge/main.nf' +include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../modules/nf-core/bcftools/merge/main.nf' +include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF } from '../../../../modules/nf-core/bcftools/merge/main.nf' workflow test_bcftools_merge { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/mpileup/main.nf b/tests/modules/nf-core/bcftools/mpileup/main.nf index 1568f157428..33e02842572 100644 --- a/tests/modules/nf-core/bcftools/mpileup/main.nf +++ b/tests/modules/nf-core/bcftools/mpileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf' +include { BCFTOOLS_MPILEUP } from '../../../../modules/nf-core/bcftools/mpileup/main.nf' workflow test_bcftools_mpileup { diff --git a/tests/modules/nf-core/bcftools/norm/main.nf b/tests/modules/nf-core/bcftools/norm/main.nf index a9ac75ba53c..cf667d65ade 100644 --- a/tests/modules/nf-core/bcftools/norm/main.nf +++ b/tests/modules/nf-core/bcftools/norm/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_NORM } from '../../../../modules/bcftools/norm/main.nf' +include { BCFTOOLS_NORM } from '../../../../modules/nf-core/bcftools/norm/main.nf' workflow test_bcftools_norm_no_tbi { diff --git a/tests/modules/nf-core/bcftools/query/main.nf b/tests/modules/nf-core/bcftools/query/main.nf index f40cb0faa7c..057a4f7c882 100644 --- a/tests/modules/nf-core/bcftools/query/main.nf +++ b/tests/modules/nf-core/bcftools/query/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_QUERY } from '../../../../modules/bcftools/query/main.nf' +include { BCFTOOLS_QUERY } from '../../../../modules/nf-core/bcftools/query/main.nf' workflow test_bcftools_query { diff --git a/tests/modules/nf-core/bcftools/reheader/main.nf b/tests/modules/nf-core/bcftools/reheader/main.nf index d1dcd8b8269..a84eba199ba 100644 --- a/tests/modules/nf-core/bcftools/reheader/main.nf +++ b/tests/modules/nf-core/bcftools/reheader/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf' +include { BCFTOOLS_REHEADER } from '../../../../modules/nf-core/bcftools/reheader/main.nf' workflow test_bcftools_reheader_update_sequences { diff --git a/tests/modules/nf-core/bcftools/roh/main.nf b/tests/modules/nf-core/bcftools/roh/main.nf index 3a2ef6402a6..b71696c78d3 100644 --- a/tests/modules/nf-core/bcftools/roh/main.nf +++ b/tests/modules/nf-core/bcftools/roh/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf' +include { BCFTOOLS_ROH } from '../../../../modules/nf-core/bcftools/roh/main.nf' workflow test_bcftools_roh { diff --git a/tests/modules/nf-core/bcftools/sort/main.nf b/tests/modules/nf-core/bcftools/sort/main.nf index fadb8270f8a..e649bb3d52f 100644 --- a/tests/modules/nf-core/bcftools/sort/main.nf +++ b/tests/modules/nf-core/bcftools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_SORT } from '../../../../modules/bcftools/sort/main.nf' +include { BCFTOOLS_SORT } from '../../../../modules/nf-core/bcftools/sort/main.nf' workflow test_bcftools_sort { diff --git a/tests/modules/nf-core/bcftools/stats/main.nf b/tests/modules/nf-core/bcftools/stats/main.nf index dbc3268ab27..59064e11851 100644 --- a/tests/modules/nf-core/bcftools/stats/main.nf +++ b/tests/modules/nf-core/bcftools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_STATS } from '../../../../modules/bcftools/stats/main.nf' +include { BCFTOOLS_STATS } from '../../../../modules/nf-core/bcftools/stats/main.nf' workflow test_bcftools_stats { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/view/main.nf b/tests/modules/nf-core/bcftools/view/main.nf index f45d0284ac8..43aa7d64895 100644 --- a/tests/modules/nf-core/bcftools/view/main.nf +++ b/tests/modules/nf-core/bcftools/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_VIEW } from '../../../../modules/bcftools/view/main.nf' +include { BCFTOOLS_VIEW } from '../../../../modules/nf-core/bcftools/view/main.nf' workflow test_bcftools_view { diff --git a/tests/modules/nf-core/bcl2fastq/main.nf b/tests/modules/nf-core/bcl2fastq/main.nf index 3564dbecc38..18ad2ef1a84 100644 --- a/tests/modules/nf-core/bcl2fastq/main.nf +++ b/tests/modules/nf-core/bcl2fastq/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCL2FASTQ } from '../../../modules/bcl2fastq/main.nf' -include { UNTAR } from '../../../modules/untar/main.nf' +include { BCL2FASTQ } from '../../../modules/nf-core/bcl2fastq/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' workflow test_bcl2fastq { ch_flowcell = Channel.value([ diff --git a/tests/modules/nf-core/bclconvert/main.nf b/tests/modules/nf-core/bclconvert/main.nf index b2ba3b8639b..aaba14bd5c1 100644 --- a/tests/modules/nf-core/bclconvert/main.nf +++ b/tests/modules/nf-core/bclconvert/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCLCONVERT } from '../../../modules/bclconvert/main.nf' -include { UNTAR } from '../../../modules/untar/main.nf' +include { BCLCONVERT } from '../../../modules/nf-core/bclconvert/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' workflow test_bclconvert { ch_flowcell = Channel.value([ diff --git a/tests/modules/nf-core/bedtools/bamtobed/main.nf b/tests/modules/nf-core/bedtools/bamtobed/main.nf index e7635a3d8b0..95aa07d21e7 100644 --- a/tests/modules/nf-core/bedtools/bamtobed/main.nf +++ b/tests/modules/nf-core/bedtools/bamtobed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_BAMTOBED } from '../../../../modules/bedtools/bamtobed/main.nf' +include { BEDTOOLS_BAMTOBED } from '../../../../modules/nf-core/bedtools/bamtobed/main.nf' workflow test_bedtools_bamtobed { input = [ [ id:'test'], //meta map diff --git a/tests/modules/nf-core/bedtools/complement/main.nf b/tests/modules/nf-core/bedtools/complement/main.nf index a1cca0330c6..01aa5e7867e 100644 --- a/tests/modules/nf-core/bedtools/complement/main.nf +++ b/tests/modules/nf-core/bedtools/complement/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_COMPLEMENT } from '../../../../modules/bedtools/complement/main.nf' +include { BEDTOOLS_COMPLEMENT } from '../../../../modules/nf-core/bedtools/complement/main.nf' workflow test_bedtools_complement { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/genomecov/main.nf b/tests/modules/nf-core/bedtools/genomecov/main.nf index b507a2cdc3d..1d151ddfb7f 100644 --- a/tests/modules/nf-core/bedtools/genomecov/main.nf +++ b/tests/modules/nf-core/bedtools/genomecov/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf' +include { BEDTOOLS_GENOMECOV } from '../../../../modules/nf-core/bedtools/genomecov/main.nf' workflow test_bedtools_genomecov_noscale { input = [ diff --git a/tests/modules/nf-core/bedtools/getfasta/main.nf b/tests/modules/nf-core/bedtools/getfasta/main.nf index 425c49d5f04..a5f018ba3d8 100644 --- a/tests/modules/nf-core/bedtools/getfasta/main.nf +++ b/tests/modules/nf-core/bedtools/getfasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_GETFASTA } from '../../../../modules/bedtools/getfasta/main.nf' +include { BEDTOOLS_GETFASTA } from '../../../../modules/nf-core/bedtools/getfasta/main.nf' workflow test_bedtools_getfasta { bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) diff --git a/tests/modules/nf-core/bedtools/intersect/main.nf b/tests/modules/nf-core/bedtools/intersect/main.nf index c17d03e6161..69dfd6e1788 100644 --- a/tests/modules/nf-core/bedtools/intersect/main.nf +++ b/tests/modules/nf-core/bedtools/intersect/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_INTERSECT } from '../../../../modules/bedtools/intersect/main.nf' +include { BEDTOOLS_INTERSECT } from '../../../../modules/nf-core/bedtools/intersect/main.nf' workflow test_bedtools_intersect { input = [ diff --git a/tests/modules/nf-core/bedtools/makewindows/main.nf b/tests/modules/nf-core/bedtools/makewindows/main.nf index ce37de725a9..e42a02b51ec 100644 --- a/tests/modules/nf-core/bedtools/makewindows/main.nf +++ b/tests/modules/nf-core/bedtools/makewindows/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf' +include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/nf-core/bedtools/makewindows/main.nf' workflow test_bedtools_makewindows { diff --git a/tests/modules/nf-core/bedtools/maskfasta/main.nf b/tests/modules/nf-core/bedtools/maskfasta/main.nf index 0da02ad3358..634d9b76fa3 100644 --- a/tests/modules/nf-core/bedtools/maskfasta/main.nf +++ b/tests/modules/nf-core/bedtools/maskfasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_MASKFASTA } from '../../../../modules/bedtools/maskfasta/main.nf' +include { BEDTOOLS_MASKFASTA } from '../../../../modules/nf-core/bedtools/maskfasta/main.nf' workflow test_bedtools_maskfasta { bed = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/merge/main.nf b/tests/modules/nf-core/bedtools/merge/main.nf index 5fca0526b40..6f5ea5e4a13 100644 --- a/tests/modules/nf-core/bedtools/merge/main.nf +++ b/tests/modules/nf-core/bedtools/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_MERGE } from '../../../../modules/bedtools/merge/main.nf' +include { BEDTOOLS_MERGE } from '../../../../modules/nf-core/bedtools/merge/main.nf' workflow test_bedtools_merge { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/slop/main.nf b/tests/modules/nf-core/bedtools/slop/main.nf index e7136fdc7be..413f420e7d9 100644 --- a/tests/modules/nf-core/bedtools/slop/main.nf +++ b/tests/modules/nf-core/bedtools/slop/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SLOP } from '../../../../modules/bedtools/slop/main.nf' +include { BEDTOOLS_SLOP } from '../../../../modules/nf-core/bedtools/slop/main.nf' workflow test_bedtools_slop { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/sort/main.nf b/tests/modules/nf-core/bedtools/sort/main.nf index 342b411673a..d35365700e7 100644 --- a/tests/modules/nf-core/bedtools/sort/main.nf +++ b/tests/modules/nf-core/bedtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SORT } from '../../../../modules/bedtools/sort/main.nf' +include { BEDTOOLS_SORT } from '../../../../modules/nf-core/bedtools/sort/main.nf' workflow test_bedtools_sort { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/split/main.nf b/tests/modules/nf-core/bedtools/split/main.nf index 7a1dc685b58..925606bcae6 100644 --- a/tests/modules/nf-core/bedtools/split/main.nf +++ b/tests/modules/nf-core/bedtools/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SPLIT } from '../../../../modules/bedtools/split/main.nf' +include { BEDTOOLS_SPLIT } from '../../../../modules/nf-core/bedtools/split/main.nf' workflow test_bedtools_split { diff --git a/tests/modules/nf-core/bedtools/subtract/main.nf b/tests/modules/nf-core/bedtools/subtract/main.nf index 2a0e6eab7ef..92056f506e4 100644 --- a/tests/modules/nf-core/bedtools/subtract/main.nf +++ b/tests/modules/nf-core/bedtools/subtract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SUBTRACT } from '../../../../modules/bedtools/subtract/main.nf' +include { BEDTOOLS_SUBTRACT } from '../../../../modules/nf-core/bedtools/subtract/main.nf' workflow test_bedtools_subtract { input = [ diff --git a/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf index aeab18b9a57..8c3666605a6 100644 --- a/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../modules/biobambam/bammarkduplicates2/main.nf' +include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../modules/nf-core/biobambam/bammarkduplicates2/main.nf' workflow test_biobambam_bammarkduplicates2 { diff --git a/tests/modules/nf-core/biobambam/bammerge/main.nf b/tests/modules/nf-core/biobambam/bammerge/main.nf index 7b4ee9cb6c8..003c570ce32 100644 --- a/tests/modules/nf-core/biobambam/bammerge/main.nf +++ b/tests/modules/nf-core/biobambam/bammerge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BIOBAMBAM_BAMMERGE } from '../../../../modules/biobambam/bammerge/main.nf' +include { BIOBAMBAM_BAMMERGE } from '../../../../modules/nf-core/biobambam/bammerge/main.nf' workflow test_biobambam_bammerge_paired { diff --git a/tests/modules/nf-core/biobambam/bamsormadup/main.nf b/tests/modules/nf-core/biobambam/bamsormadup/main.nf index 9bcb1cf3671..3afcf9a8438 100644 --- a/tests/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/tests/modules/nf-core/biobambam/bamsormadup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf' +include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/nf-core/biobambam/bamsormadup/main.nf' workflow test_biobambam_bamsormadup_multi_input { diff --git a/tests/modules/nf-core/biscuit/align/main.nf b/tests/modules/nf-core/biscuit/align/main.nf index f3e3cb649cc..7e3c91a3a74 100644 --- a/tests/modules/nf-core/biscuit/align/main.nf +++ b/tests/modules/nf-core/biscuit/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../modules/biscuit/align/main.nf' -include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../modules/biscuit/align/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../modules/nf-core/biscuit/align/main.nf' +include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../modules/nf-core/biscuit/align/main.nf' // Single-end test diff --git a/tests/modules/nf-core/biscuit/biscuitblaster/main.nf b/tests/modules/nf-core/biscuit/biscuitblaster/main.nf index 5e4bc95a999..fe15d373732 100644 --- a/tests/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/tests/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../modules/biscuit/biscuitblaster/main.nf' -include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../modules/biscuit/biscuitblaster/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../modules/nf-core/biscuit/biscuitblaster/main.nf' +include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../modules/nf-core/biscuit/biscuitblaster/main.nf' // Single-end test workflow test_biscuit_blaster_single { diff --git a/tests/modules/nf-core/biscuit/bsconv/main.nf b/tests/modules/nf-core/biscuit/bsconv/main.nf index f73388691fa..0de88274a9f 100644 --- a/tests/modules/nf-core/biscuit/bsconv/main.nf +++ b/tests/modules/nf-core/biscuit/bsconv/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_BSCONV } from '../../../../modules/biscuit/bsconv/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_BSCONV } from '../../../../modules/nf-core/biscuit/bsconv/main.nf' workflow test_biscuit_bsconv { diff --git a/tests/modules/nf-core/biscuit/epiread/main.nf b/tests/modules/nf-core/biscuit/epiread/main.nf index 54a73ae3ad1..243744edc1a 100644 --- a/tests/modules/nf-core/biscuit/epiread/main.nf +++ b/tests/modules/nf-core/biscuit/epiread/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_EPIREAD } from '../../../../modules/biscuit/epiread/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_EPIREAD } from '../../../../modules/nf-core/biscuit/epiread/main.nf' workflow test_biscuit_epiread_nosnp { diff --git a/tests/modules/nf-core/biscuit/index/main.nf b/tests/modules/nf-core/biscuit/index/main.nf index c13d441bf00..8d4cfd857cf 100644 --- a/tests/modules/nf-core/biscuit/index/main.nf +++ b/tests/modules/nf-core/biscuit/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' workflow test_biscuit_index { diff --git a/tests/modules/nf-core/biscuit/mergecg/main.nf b/tests/modules/nf-core/biscuit/mergecg/main.nf index 7d51f3b89bf..edb36d46183 100644 --- a/tests/modules/nf-core/biscuit/mergecg/main.nf +++ b/tests/modules/nf-core/biscuit/mergecg/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_MERGECG } from '../../../../modules/biscuit/mergecg/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_MERGECG } from '../../../../modules/nf-core/biscuit/mergecg/main.nf' workflow test_biscuit_mergecg { diff --git a/tests/modules/nf-core/biscuit/pileup/main.nf b/tests/modules/nf-core/biscuit/pileup/main.nf index cf1914ece5c..74b1eb26f56 100644 --- a/tests/modules/nf-core/biscuit/pileup/main.nf +++ b/tests/modules/nf-core/biscuit/pileup/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_PILEUP } from '../../../../modules/biscuit/pileup/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_PILEUP } from '../../../../modules/nf-core/biscuit/pileup/main.nf' workflow test_biscuit_pileup { diff --git a/tests/modules/nf-core/biscuit/qc/main.nf b/tests/modules/nf-core/biscuit/qc/main.nf index 7c6d61cd63b..5752b19f3f3 100644 --- a/tests/modules/nf-core/biscuit/qc/main.nf +++ b/tests/modules/nf-core/biscuit/qc/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf' -include { BISCUIT_QC } from '../../../../modules/biscuit/qc/main.nf' +include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_QC } from '../../../../modules/nf-core/biscuit/qc/main.nf' workflow test_biscuit_qc { diff --git a/tests/modules/nf-core/biscuit/vcf2bed/main.nf b/tests/modules/nf-core/biscuit/vcf2bed/main.nf index 25597d49bdf..a69ff548782 100644 --- a/tests/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/tests/modules/nf-core/biscuit/vcf2bed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISCUIT_VCF2BED } from '../../../../modules/biscuit/vcf2bed/main.nf' +include { BISCUIT_VCF2BED } from '../../../../modules/nf-core/biscuit/vcf2bed/main.nf' workflow test_biscuit_vcf2bed { diff --git a/tests/modules/nf-core/bismark/align/main.nf b/tests/modules/nf-core/bismark/align/main.nf index fe6d616a4c1..6823b581a0e 100644 --- a/tests/modules/nf-core/bismark/align/main.nf +++ b/tests/modules/nf-core/bismark/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' -include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../modules/bismark/align/main.nf' -include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../modules/bismark/align/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../modules/nf-core/bismark/align/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bismark/deduplicate/main.nf b/tests/modules/nf-core/bismark/deduplicate/main.nf index ad97d66aad3..0e90444361d 100644 --- a/tests/modules/nf-core/bismark/deduplicate/main.nf +++ b/tests/modules/nf-core/bismark/deduplicate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' +include { BISMARK_DEDUPLICATE } from '../../../../modules/nf-core/bismark/deduplicate/main.nf' workflow test_bismark_deduplicate { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/bismark/genomepreparation/main.nf b/tests/modules/nf-core/bismark/genomepreparation/main.nf index a9111af3b68..60a69ff47e4 100644 --- a/tests/modules/nf-core/bismark/genomepreparation/main.nf +++ b/tests/modules/nf-core/bismark/genomepreparation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' workflow test_bismark_genomepreparation { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bismark/methylationextractor/main.nf b/tests/modules/nf-core/bismark/methylationextractor/main.nf index ed857fe8d84..7b529bb8dad 100644 --- a/tests/modules/nf-core/bismark/methylationextractor/main.nf +++ b/tests/modules/nf-core/bismark/methylationextractor/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/nf-core/bismark/methylationextractor/main.nf' workflow test_bismark_methylationextractor { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/bismark/report/main.nf b/tests/modules/nf-core/bismark/report/main.nf index f80fb2bc6c7..6451ae684c7 100644 --- a/tests/modules/nf-core/bismark/report/main.nf +++ b/tests/modules/nf-core/bismark/report/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' -include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf' -include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' -include { BISMARK_REPORT } from '../../../../modules/bismark/report/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_ALIGN } from '../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_DEDUPLICATE } from '../../../../modules/nf-core/bismark/deduplicate/main.nf' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/nf-core/bismark/methylationextractor/main.nf' +include { BISMARK_REPORT } from '../../../../modules/nf-core/bismark/report/main.nf' workflow test_bismark_report { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/bismark/summary/main.nf b/tests/modules/nf-core/bismark/summary/main.nf index 8eabe51f7b6..e1b78ff7464 100644 --- a/tests/modules/nf-core/bismark/summary/main.nf +++ b/tests/modules/nf-core/bismark/summary/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' -include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf' -include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' -include { BISMARK_SUMMARY } from '../../../../modules/bismark/summary/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_ALIGN } from '../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_DEDUPLICATE } from '../../../../modules/nf-core/bismark/deduplicate/main.nf' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/nf-core/bismark/methylationextractor/main.nf' +include { BISMARK_SUMMARY } from '../../../../modules/nf-core/bismark/summary/main.nf' workflow test_bismark_summary { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/blast/blastn/main.nf b/tests/modules/nf-core/blast/blastn/main.nf index 3c8496dc609..074cb6a3162 100644 --- a/tests/modules/nf-core/blast/blastn/main.nf +++ b/tests/modules/nf-core/blast/blastn/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf' -include { BLAST_BLASTN } from '../../../../modules/blast/blastn/main.nf' +include { BLAST_MAKEBLASTDB } from '../../../../modules/nf-core/blast/makeblastdb/main.nf' +include { BLAST_BLASTN } from '../../../../modules/nf-core/blast/blastn/main.nf' workflow test_blast_blastn { input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/blast/makeblastdb/main.nf b/tests/modules/nf-core/blast/makeblastdb/main.nf index 9d778457e9f..f8fb262c1eb 100644 --- a/tests/modules/nf-core/blast/makeblastdb/main.nf +++ b/tests/modules/nf-core/blast/makeblastdb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf' +include { BLAST_MAKEBLASTDB } from '../../../../modules/nf-core/blast/makeblastdb/main.nf' workflow test_blast_makeblastdb { input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/blast/tblastn/main.nf b/tests/modules/nf-core/blast/tblastn/main.nf index 6d343660193..7fd65f94293 100644 --- a/tests/modules/nf-core/blast/tblastn/main.nf +++ b/tests/modules/nf-core/blast/tblastn/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BLAST_TBLASTN } from '../../../../modules/blast/tblastn/main.nf' -include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf' +include { BLAST_TBLASTN } from '../../../../modules/nf-core/blast/tblastn/main.nf' +include { BLAST_MAKEBLASTDB } from '../../../../modules/nf-core/blast/makeblastdb/main.nf' workflow test_blast_tblastn { diff --git a/tests/modules/nf-core/bowtie/align/main.nf b/tests/modules/nf-core/bowtie/align/main.nf index e773cd38cef..85a58d019ea 100644 --- a/tests/modules/nf-core/bowtie/align/main.nf +++ b/tests/modules/nf-core/bowtie/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' -include { BOWTIE_ALIGN } from '../../../../modules/bowtie/align/main.nf' +include { BOWTIE_BUILD } from '../../../../modules/nf-core/bowtie/build/main.nf' +include { BOWTIE_ALIGN } from '../../../../modules/nf-core/bowtie/align/main.nf' workflow test_bowtie_align_single_end { input = [ diff --git a/tests/modules/nf-core/bowtie/build_test/main.nf b/tests/modules/nf-core/bowtie/build_test/main.nf index 7a36fb5582f..eb0c3dd930f 100644 --- a/tests/modules/nf-core/bowtie/build_test/main.nf +++ b/tests/modules/nf-core/bowtie/build_test/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' +include { BOWTIE_BUILD } from '../../../../modules/nf-core/bowtie/build/main.nf' workflow test_bowtie_build { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bowtie2/align/main.nf b/tests/modules/nf-core/bowtie2/align/main.nf index 4f08b53304f..0645d198a63 100644 --- a/tests/modules/nf-core/bowtie2/align/main.nf +++ b/tests/modules/nf-core/bowtie2/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' -include { BOWTIE2_ALIGN } from '../../../../modules/bowtie2/align/main.nf' +include { BOWTIE2_BUILD } from '../../../../modules/nf-core/bowtie2/build/main.nf' +include { BOWTIE2_ALIGN } from '../../../../modules/nf-core/bowtie2/align/main.nf' workflow test_bowtie2_align_single_end { input = [ diff --git a/tests/modules/nf-core/bowtie2/build_test/main.nf b/tests/modules/nf-core/bowtie2/build_test/main.nf index f1d35083c80..c2042c0fd1c 100644 --- a/tests/modules/nf-core/bowtie2/build_test/main.nf +++ b/tests/modules/nf-core/bowtie2/build_test/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' +include { BOWTIE2_BUILD } from '../../../../modules/nf-core/bowtie2/build/main.nf' workflow test_bowtie2_build { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bracken/bracken/main.nf b/tests/modules/nf-core/bracken/bracken/main.nf index 190aeb7051e..fda8efab40b 100644 --- a/tests/modules/nf-core/bracken/bracken/main.nf +++ b/tests/modules/nf-core/bracken/bracken/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf' -include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main.nf' +include { BRACKEN_BRACKEN } from '../../../../modules/nf-core/bracken/bracken/main.nf' workflow test_bracken_bracken_single_end_default_args { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf index d382d907179..aea65aebbbe 100644 --- a/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf' -include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf' -include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/bracken/combinebrackenoutputs/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main.nf' +include { BRACKEN_BRACKEN } from '../../../../modules/nf-core/bracken/bracken/main.nf' +include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/nf-core/bracken/combinebrackenoutputs/main.nf' workflow test_bracken_combinebrackenoutputs { diff --git a/tests/modules/nf-core/busco/main.nf b/tests/modules/nf-core/busco/main.nf index 2313bd06a82..30176d486a3 100644 --- a/tests/modules/nf-core/busco/main.nf +++ b/tests/modules/nf-core/busco/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BUSCO } from '../../../modules/busco/main.nf' +include { BUSCO } from '../../../modules/nf-core/busco/main.nf' workflow test_busco_genome_single_fasta { diff --git a/tests/modules/nf-core/bwa/aln/main.nf b/tests/modules/nf-core/bwa/aln/main.nf index 909e7a2d849..92d899f4648 100644 --- a/tests/modules/nf-core/bwa/aln/main.nf +++ b/tests/modules/nf-core/bwa/aln/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' -include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_ALN } from '../../../../modules/nf-core/bwa/aln/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwa/index/main.nf b/tests/modules/nf-core/bwa/index/main.nf index fe040cb22ed..4426f94066b 100644 --- a/tests/modules/nf-core/bwa/index/main.nf +++ b/tests/modules/nf-core/bwa/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' workflow test_bwa_index { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bwa/mem/main.nf b/tests/modules/nf-core/bwa/mem/main.nf index c9c57197048..34e6a6732c6 100644 --- a/tests/modules/nf-core/bwa/mem/main.nf +++ b/tests/modules/nf-core/bwa/mem/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' -include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM } from '../../../../modules/nf-core/bwa/mem/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwa/sampe/main.nf b/tests/modules/nf-core/bwa/sampe/main.nf index abd25566a42..e57a26ae104 100644 --- a/tests/modules/nf-core/bwa/sampe/main.nf +++ b/tests/modules/nf-core/bwa/sampe/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' -include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' -include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_ALN } from '../../../../modules/nf-core/bwa/aln/main.nf' +include { BWA_SAMPE } from '../../../../modules/nf-core/bwa/sampe/main.nf' workflow test_bwa_sampe { diff --git a/tests/modules/nf-core/bwa/samse/main.nf b/tests/modules/nf-core/bwa/samse/main.nf index 17912c36b0d..283fed3e63c 100644 --- a/tests/modules/nf-core/bwa/samse/main.nf +++ b/tests/modules/nf-core/bwa/samse/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' -include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' -include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_ALN } from '../../../../modules/nf-core/bwa/aln/main.nf' +include { BWA_SAMSE } from '../../../../modules/nf-core/bwa/samse/main.nf' workflow test_bwa_samse { diff --git a/tests/modules/nf-core/bwamem2/index/main.nf b/tests/modules/nf-core/bwamem2/index/main.nf index eca045e257c..79706edeb1b 100644 --- a/tests/modules/nf-core/bwamem2/index/main.nf +++ b/tests/modules/nf-core/bwamem2/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' +include { BWAMEM2_INDEX } from '../../../../modules/nf-core/bwamem2/index/main.nf' workflow test_bwamem2_index { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bwamem2/mem/main.nf b/tests/modules/nf-core/bwamem2/mem/main.nf index 386bf5319eb..39159a454bf 100644 --- a/tests/modules/nf-core/bwamem2/mem/main.nf +++ b/tests/modules/nf-core/bwamem2/mem/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' -include { BWAMEM2_MEM } from '../../../../modules/bwamem2/mem/main.nf' +include { BWAMEM2_INDEX } from '../../../../modules/nf-core/bwamem2/index/main.nf' +include { BWAMEM2_MEM } from '../../../../modules/nf-core/bwamem2/mem/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwameth/align/main.nf b/tests/modules/nf-core/bwameth/align/main.nf index 8066941c359..0c1a7db70a6 100644 --- a/tests/modules/nf-core/bwameth/align/main.nf +++ b/tests/modules/nf-core/bwameth/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' -include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf' +include { BWAMETH_INDEX } from '../../../../modules/nf-core/bwameth/index/main.nf' +include { BWAMETH_ALIGN } from '../../../../modules/nf-core/bwameth/align/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwameth/index/main.nf b/tests/modules/nf-core/bwameth/index/main.nf index b70fd1f7967..b65969b745d 100644 --- a/tests/modules/nf-core/bwameth/index/main.nf +++ b/tests/modules/nf-core/bwameth/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' +include { BWAMETH_INDEX } from '../../../../modules/nf-core/bwameth/index/main.nf' workflow test_bwameth_index { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/cat/cat/main.nf b/tests/modules/nf-core/cat/cat/main.nf index 24e1d00df55..ff12494b3c4 100644 --- a/tests/modules/nf-core/cat/cat/main.nf +++ b/tests/modules/nf-core/cat/cat/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CAT_CAT } from '../../../../modules/cat/cat/main.nf' -include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/cat/cat/main.nf' -include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/cat/cat/main.nf' +include { CAT_CAT } from '../../../../modules/nf-core/cat/cat/main.nf' +include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/nf-core/cat/cat/main.nf' +include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/nf-core/cat/cat/main.nf' workflow test_cat_unzipped_unzipped { diff --git a/tests/modules/nf-core/cat/fastq/main.nf b/tests/modules/nf-core/cat/fastq/main.nf index 671d01e2da1..1e0037968db 100644 --- a/tests/modules/nf-core/cat/fastq/main.nf +++ b/tests/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf' +include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main.nf' workflow test_cat_fastq_single_end { input = [ diff --git a/tests/modules/nf-core/cellranger/count/main.nf b/tests/modules/nf-core/cellranger/count/main.nf index bb9e11d1b9f..1e1133af50b 100644 --- a/tests/modules/nf-core/cellranger/count/main.nf +++ b/tests/modules/nf-core/cellranger/count/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf' -include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf' -include { CELLRANGER_COUNT } from '../../../../modules/cellranger/count/main.nf' +include { CELLRANGER_MKGTF } from '../../../../modules/nf-core/cellranger/mkgtf/main.nf' +include { CELLRANGER_MKREF } from '../../../../modules/nf-core/cellranger/mkref/main.nf' +include { CELLRANGER_COUNT } from '../../../../modules/nf-core/cellranger/count/main.nf' workflow test_cellranger_count { diff --git a/tests/modules/nf-core/cellranger/mkfastq/main.nf b/tests/modules/nf-core/cellranger/mkfastq/main.nf index 7bad0feca80..486b33cc428 100644 --- a/tests/modules/nf-core/cellranger/mkfastq/main.nf +++ b/tests/modules/nf-core/cellranger/mkfastq/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { CELLRANGER_MKFASTQ } from '../../../../modules/cellranger/mkfastq/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CELLRANGER_MKFASTQ } from '../../../../modules/nf-core/cellranger/mkfastq/main.nf' workflow test_cellranger_mkfastq_simple { diff --git a/tests/modules/nf-core/cellranger/mkgtf/main.nf b/tests/modules/nf-core/cellranger/mkgtf/main.nf index 19e2cba0d30..7dad0e3147a 100644 --- a/tests/modules/nf-core/cellranger/mkgtf/main.nf +++ b/tests/modules/nf-core/cellranger/mkgtf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf' +include { CELLRANGER_MKGTF } from '../../../../modules/nf-core/cellranger/mkgtf/main.nf' workflow test_cellranger_mkgtf { gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) diff --git a/tests/modules/nf-core/cellranger/mkref/main.nf b/tests/modules/nf-core/cellranger/mkref/main.nf index ad98ed1a73c..7063715ae04 100644 --- a/tests/modules/nf-core/cellranger/mkref/main.nf +++ b/tests/modules/nf-core/cellranger/mkref/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf' +include { CELLRANGER_MKREF } from '../../../../modules/nf-core/cellranger/mkref/main.nf' workflow test_cellranger_mkref { diff --git a/tests/modules/nf-core/centrifuge/centrifuge/main.nf b/tests/modules/nf-core/centrifuge/centrifuge/main.nf index 35deeb583f6..860378b31a2 100644 --- a/tests/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/tests/modules/nf-core/centrifuge/centrifuge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/nf-core/centrifuge/centrifuge/main.nf' workflow test_centrifuge_centrifuge_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/centrifuge/kreport/main.nf b/tests/modules/nf-core/centrifuge/kreport/main.nf index 397d33aa18a..f7e3c29b7f2 100644 --- a/tests/modules/nf-core/centrifuge/kreport/main.nf +++ b/tests/modules/nf-core/centrifuge/kreport/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf' -include { CENTRIFUGE_KREPORT } from '../../../../modules/centrifuge/kreport/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/nf-core/centrifuge/centrifuge/main.nf' +include { CENTRIFUGE_KREPORT } from '../../../../modules/nf-core/centrifuge/kreport/main.nf' workflow test_centrifuge_kreport_single_end { diff --git a/tests/modules/nf-core/checkm/lineagewf/main.nf b/tests/modules/nf-core/checkm/lineagewf/main.nf index cb7c7baec5b..53fb44efe2e 100644 --- a/tests/modules/nf-core/checkm/lineagewf/main.nf +++ b/tests/modules/nf-core/checkm/lineagewf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf' +include { CHECKM_LINEAGEWF } from '../../../../modules/nf-core/checkm/lineagewf/main.nf' workflow test_checkm_lineagewf { diff --git a/tests/modules/nf-core/checkm/qa/main.nf b/tests/modules/nf-core/checkm/qa/main.nf index 2be2dd67898..035d9cda56b 100644 --- a/tests/modules/nf-core/checkm/qa/main.nf +++ b/tests/modules/nf-core/checkm/qa/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf' -include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA } from '../../../../modules/checkm/lineagewf/main.nf' -include { CHECKM_QA } from '../../../../modules/checkm/qa/main.nf' -include { CHECKM_QA as CHECKM_QA_FASTA } from '../../../../modules/checkm/qa/main.nf' +include { CHECKM_LINEAGEWF } from '../../../../modules/nf-core/checkm/lineagewf/main.nf' +include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA } from '../../../../modules/nf-core/checkm/lineagewf/main.nf' +include { CHECKM_QA } from '../../../../modules/nf-core/checkm/qa/main.nf' +include { CHECKM_QA as CHECKM_QA_FASTA } from '../../../../modules/nf-core/checkm/qa/main.nf' workflow test_checkm_qa { diff --git a/tests/modules/nf-core/chromap/chromap/main.nf b/tests/modules/nf-core/chromap/chromap/main.nf index 5522f2b5f39..30d73410eee 100644 --- a/tests/modules/nf-core/chromap/chromap/main.nf +++ b/tests/modules/nf-core/chromap/chromap/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf' -include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/chromap/chromap/main.nf' -include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../modules/chromap/chromap/main.nf' +include { CHROMAP_INDEX } from '../../../../modules/nf-core/chromap/index/main.nf' +include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/nf-core/chromap/chromap/main.nf' +include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../modules/nf-core/chromap/chromap/main.nf' workflow test_chromap_chromap_single_end { diff --git a/tests/modules/nf-core/chromap/index/main.nf b/tests/modules/nf-core/chromap/index/main.nf index 18b4200627b..c649e12511a 100644 --- a/tests/modules/nf-core/chromap/index/main.nf +++ b/tests/modules/nf-core/chromap/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf' +include { CHROMAP_INDEX } from '../../../../modules/nf-core/chromap/index/main.nf' workflow test_chromap_index { diff --git a/tests/modules/nf-core/clonalframeml/main.nf b/tests/modules/nf-core/clonalframeml/main.nf index 73773113479..2ee14d56a5f 100644 --- a/tests/modules/nf-core/clonalframeml/main.nf +++ b/tests/modules/nf-core/clonalframeml/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CLONALFRAMEML } from '../../../modules/clonalframeml/main.nf' +include { CLONALFRAMEML } from '../../../modules/nf-core/clonalframeml/main.nf' workflow test_clonalframeml { diff --git a/tests/modules/nf-core/cmseq/polymut/main.nf b/tests/modules/nf-core/cmseq/polymut/main.nf index df6a0ac13ef..b92115bd20e 100644 --- a/tests/modules/nf-core/cmseq/polymut/main.nf +++ b/tests/modules/nf-core/cmseq/polymut/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CMSEQ_POLYMUT } from '../../../../modules/cmseq/polymut/main.nf' +include { CMSEQ_POLYMUT } from '../../../../modules/nf-core/cmseq/polymut/main.nf' workflow test_cmseq_polymut_1 { diff --git a/tests/modules/nf-core/cnvkit/antitarget/main.nf b/tests/modules/nf-core/cnvkit/antitarget/main.nf index 44e49eb2123..b4bc6c1be9d 100644 --- a/tests/modules/nf-core/cnvkit/antitarget/main.nf +++ b/tests/modules/nf-core/cnvkit/antitarget/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVKIT_ANTITARGET } from '../../../../modules/cnvkit/antitarget/main.nf' +include { CNVKIT_ANTITARGET } from '../../../../modules/nf-core/cnvkit/antitarget/main.nf' workflow test_cnvkit_antitarget { diff --git a/tests/modules/nf-core/cnvkit/batch/main.nf b/tests/modules/nf-core/cnvkit/batch/main.nf index daf87a37cb1..492e3585e94 100755 --- a/tests/modules/nf-core/cnvkit/batch/main.nf +++ b/tests/modules/nf-core/cnvkit/batch/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf' -include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf' -include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf' -include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/nf-core/cnvkit/batch/main.nf' workflow test_cnvkit_hybrid_somatic { diff --git a/tests/modules/nf-core/cnvkit/reference/main.nf b/tests/modules/nf-core/cnvkit/reference/main.nf index a72ad56646a..650bc8b0258 100644 --- a/tests/modules/nf-core/cnvkit/reference/main.nf +++ b/tests/modules/nf-core/cnvkit/reference/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVKIT_REFERENCE } from '../../../../modules/cnvkit/reference/main.nf' +include { CNVKIT_REFERENCE } from '../../../../modules/nf-core/cnvkit/reference/main.nf' workflow test_cnvkit_reference { diff --git a/tests/modules/nf-core/cnvpytor/callcnvs/main.nf b/tests/modules/nf-core/cnvpytor/callcnvs/main.nf index 96d3325067a..a580c637fd5 100644 --- a/tests/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/tests/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_CALLCNVS } from '../../../../modules/cnvpytor/callcnvs/main.nf' +include { CNVPYTOR_CALLCNVS } from '../../../../modules/nf-core/cnvpytor/callcnvs/main.nf' workflow test_cnvpytor_callcnvs { diff --git a/tests/modules/nf-core/cnvpytor/histogram/main.nf b/tests/modules/nf-core/cnvpytor/histogram/main.nf index 2178dee1f6b..a50cf1974dc 100644 --- a/tests/modules/nf-core/cnvpytor/histogram/main.nf +++ b/tests/modules/nf-core/cnvpytor/histogram/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_HISTOGRAM } from '../../../../modules/cnvpytor/histogram/main.nf' +include { CNVPYTOR_HISTOGRAM } from '../../../../modules/nf-core/cnvpytor/histogram/main.nf' workflow test_cnvpytor_histogram { diff --git a/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf b/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf index 0d9be324fe3..3b9e9b04a24 100644 --- a/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../modules/cnvpytor/importreaddepth/main.nf' +include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../modules/nf-core/cnvpytor/importreaddepth/main.nf' workflow test_cnvpytor_importreaddepth { diff --git a/tests/modules/nf-core/cnvpytor/partition/main.nf b/tests/modules/nf-core/cnvpytor/partition/main.nf index cd8063a46ee..7fe24522106 100644 --- a/tests/modules/nf-core/cnvpytor/partition/main.nf +++ b/tests/modules/nf-core/cnvpytor/partition/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_PARTITION } from '../../../../modules/cnvpytor/partition/main.nf' +include { CNVPYTOR_PARTITION } from '../../../../modules/nf-core/cnvpytor/partition/main.nf' workflow test_cnvpytor_partition { diff --git a/tests/modules/nf-core/cnvpytor/view/main.nf b/tests/modules/nf-core/cnvpytor/view/main.nf index 3b99c3140e1..9ffdc6a074a 100644 --- a/tests/modules/nf-core/cnvpytor/view/main.nf +++ b/tests/modules/nf-core/cnvpytor/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_VIEW } from '../../../../modules/cnvpytor/view/main.nf' +include { CNVPYTOR_VIEW } from '../../../../modules/nf-core/cnvpytor/view/main.nf' workflow test_cnvpytor_view { diff --git a/tests/modules/nf-core/controlfreec/assesssignificance/main.nf b/tests/modules/nf-core/controlfreec/assesssignificance/main.nf index e5ed1bf73d2..c3fb2cb40e9 100644 --- a/tests/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/tests/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/controlfreec/assesssignificance/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/untar/main.nf' +include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/nf-core/controlfreec/assesssignificance/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_assesssignificance { diff --git a/tests/modules/nf-core/controlfreec/freec/main.nf b/tests/modules/nf-core/controlfreec/freec/main.nf index 1f4a069b95b..b7c01a2dd46 100644 --- a/tests/modules/nf-core/controlfreec/freec/main.nf +++ b/tests/modules/nf-core/controlfreec/freec/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/untar/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_freec { diff --git a/tests/modules/nf-core/controlfreec/freec2bed/main.nf b/tests/modules/nf-core/controlfreec/freec2bed/main.nf index c1b0f04edd4..f0e0d41fd8f 100644 --- a/tests/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/tests/modules/nf-core/controlfreec/freec2bed/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_FREEC2BED } from '../../../../modules/controlfreec/freec2bed/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/untar/main.nf' +include { CONTROLFREEC_FREEC2BED } from '../../../../modules/nf-core/controlfreec/freec2bed/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_freec2bed { diff --git a/tests/modules/nf-core/controlfreec/freec2circos/main.nf b/tests/modules/nf-core/controlfreec/freec2circos/main.nf index 6b34edb6bb6..32cfda5f2ec 100644 --- a/tests/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/tests/modules/nf-core/controlfreec/freec2circos/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../modules/controlfreec/freec2circos/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/untar/main.nf' +include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../modules/nf-core/controlfreec/freec2circos/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_freec2circos { diff --git a/tests/modules/nf-core/controlfreec/makegraph/main.nf b/tests/modules/nf-core/controlfreec/makegraph/main.nf index 543216e15b9..2ff569578e0 100644 --- a/tests/modules/nf-core/controlfreec/makegraph/main.nf +++ b/tests/modules/nf-core/controlfreec/makegraph/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/controlfreec/makegraph/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/untar/main.nf' +include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/nf-core/controlfreec/makegraph/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_makegraph { diff --git a/tests/modules/nf-core/cooler/cload/main.nf b/tests/modules/nf-core/cooler/cload/main.nf index 170b7e1199d..a01e62e082c 100644 --- a/tests/modules/nf-core/cooler/cload/main.nf +++ b/tests/modules/nf-core/cooler/cload/main.nf @@ -2,12 +2,12 @@ nextflow.enable.dsl = 2 -include { COOLER_CLOAD } from '../../../../modules/cooler/cload/main.nf' -include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/cooler/cload/main.nf' -include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/cooler/cload/main.nf' -include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' -include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../modules/cooler/dump/main.nf' -include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../modules/cooler/dump/main.nf' +include { COOLER_CLOAD } from '../../../../modules/nf-core/cooler/cload/main.nf' +include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/nf-core/cooler/cload/main.nf' +include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/nf-core/cooler/cload/main.nf' +include { COOLER_DUMP } from '../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../modules/nf-core/cooler/dump/main.nf' workflow test_cooler_cload_pairix { diff --git a/tests/modules/nf-core/cooler/digest/main.nf b/tests/modules/nf-core/cooler/digest/main.nf index 4dfa25be9bd..e681d9d690b 100644 --- a/tests/modules/nf-core/cooler/digest/main.nf +++ b/tests/modules/nf-core/cooler/digest/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { COOLER_DIGEST } from '../../../../modules/cooler/digest/main.nf' +include { COOLER_DIGEST } from '../../../../modules/nf-core/cooler/digest/main.nf' workflow test_cooler_digest { diff --git a/tests/modules/nf-core/cooler/dump/main.nf b/tests/modules/nf-core/cooler/dump/main.nf index d80ee0d76d7..b93fe88b6fc 100644 --- a/tests/modules/nf-core/cooler/dump/main.nf +++ b/tests/modules/nf-core/cooler/dump/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' +include { COOLER_DUMP } from '../../../../modules/nf-core/cooler/dump/main.nf' workflow test_cooler_dump { diff --git a/tests/modules/nf-core/cooler/merge/main.nf b/tests/modules/nf-core/cooler/merge/main.nf index 81336984926..294ef760db4 100644 --- a/tests/modules/nf-core/cooler/merge/main.nf +++ b/tests/modules/nf-core/cooler/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { COOLER_MERGE } from '../../../../modules/cooler/merge/main.nf' -include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' +include { COOLER_MERGE } from '../../../../modules/nf-core/cooler/merge/main.nf' +include { COOLER_DUMP } from '../../../../modules/nf-core/cooler/dump/main.nf' workflow test_cooler_merge { diff --git a/tests/modules/nf-core/cooler/zoomify/main.nf b/tests/modules/nf-core/cooler/zoomify/main.nf index 42edadb8c60..1e21f18f994 100644 --- a/tests/modules/nf-core/cooler/zoomify/main.nf +++ b/tests/modules/nf-core/cooler/zoomify/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { COOLER_ZOOMIFY } from '../../../../modules/cooler/zoomify/main.nf' +include { COOLER_ZOOMIFY } from '../../../../modules/nf-core/cooler/zoomify/main.nf' workflow test_cooler_zoomify { diff --git a/tests/modules/nf-core/csvtk/concat/main.nf b/tests/modules/nf-core/csvtk/concat/main.nf index aee31679052..606a5659e92 100644 --- a/tests/modules/nf-core/csvtk/concat/main.nf +++ b/tests/modules/nf-core/csvtk/concat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CSVTK_CONCAT } from '../../../../modules/csvtk/concat/main.nf' +include { CSVTK_CONCAT } from '../../../../modules/nf-core/csvtk/concat/main.nf' workflow test_csvtk_concat { diff --git a/tests/modules/nf-core/csvtk/split/main.nf b/tests/modules/nf-core/csvtk/split/main.nf index 31d24d61596..14e78bb535e 100644 --- a/tests/modules/nf-core/csvtk/split/main.nf +++ b/tests/modules/nf-core/csvtk/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CSVTK_SPLIT } from '../../../../modules/csvtk/split/main.nf' +include { CSVTK_SPLIT } from '../../../../modules/nf-core/csvtk/split/main.nf' workflow test_csvtk_split_tsv { diff --git a/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf b/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf index a9e532d26d1..6b50b4fe636 100644 --- a/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTQC } from '../../../../modules/fastqc/main.nf' -include { MULTIQC } from '../../../../modules/multiqc/main.nf' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf' +include { FASTQC } from '../../../../modules/nf-core/fastqc/main.nf' +include { MULTIQC } from '../../../../modules/nf-core/multiqc/main.nf' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/nf-core/custom/dumpsoftwareversions/main.nf' workflow fastqc1 { take: diff --git a/tests/modules/nf-core/custom/getchromsizes/main.nf b/tests/modules/nf-core/custom/getchromsizes/main.nf index 0294b8747f1..d0604def671 100644 --- a/tests/modules/nf-core/custom/getchromsizes/main.nf +++ b/tests/modules/nf-core/custom/getchromsizes/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CUSTOM_GETCHROMSIZES } from '../../../../modules/custom/getchromsizes/main.nf' +include { CUSTOM_GETCHROMSIZES } from '../../../../modules/nf-core/custom/getchromsizes/main.nf' workflow test_custom_getchromsizes { diff --git a/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf b/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf index 9f49f20e47a..831a8f36a5e 100644 --- a/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/custom/sratoolsncbisettings/main.nf' +include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/nf-core/custom/sratoolsncbisettings/main.nf' workflow test_sratoolsncbisettings_with_good_existing { diff --git a/tests/modules/nf-core/cutadapt/main.nf b/tests/modules/nf-core/cutadapt/main.nf index a47feebba8d..2a986586441 100644 --- a/tests/modules/nf-core/cutadapt/main.nf +++ b/tests/modules/nf-core/cutadapt/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CUTADAPT } from '../../../modules/cutadapt/main.nf' +include { CUTADAPT } from '../../../modules/nf-core/cutadapt/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/damageprofiler/main.nf b/tests/modules/nf-core/damageprofiler/main.nf index 9207caf1504..f4be3ddad24 100644 --- a/tests/modules/nf-core/damageprofiler/main.nf +++ b/tests/modules/nf-core/damageprofiler/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DAMAGEPROFILER } from '../../../modules/damageprofiler/main.nf' +include { DAMAGEPROFILER } from '../../../modules/nf-core/damageprofiler/main.nf' workflow test_damageprofiler { diff --git a/tests/modules/nf-core/dastool/dastool/main.nf b/tests/modules/nf-core/dastool/dastool/main.nf index 9853e724b16..5327755a76d 100644 --- a/tests/modules/nf-core/dastool/dastool/main.nf +++ b/tests/modules/nf-core/dastool/dastool/main.nf @@ -1,10 +1,10 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf' -include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf' +include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf' +include { DASTOOL_DASTOOL } from '../../../../modules/nf-core/dastool/dastool/main.nf' workflow test_dastool_dastool { diff --git a/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf b/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf index 0178dbf9e92..ef27da91d93 100644 --- a/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../../modules/gunzip/main.nf' -include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf' workflow test_dastool_fastatocontig2bin { diff --git a/tests/modules/nf-core/dastool/scaffolds2bin/main.nf b/tests/modules/nf-core/dastool/scaffolds2bin/main.nf index c45a6f2ba6b..7fc81d90ccd 100644 --- a/tests/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/tests/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../../modules/gunzip/main.nf' -include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/nf-core/dastool/scaffolds2bin/main.nf' workflow test_dastool_scaffolds2bin { diff --git a/tests/modules/nf-core/dedup/main.nf b/tests/modules/nf-core/dedup/main.nf index 4a397eaa7c5..5e2eb5a63f8 100644 --- a/tests/modules/nf-core/dedup/main.nf +++ b/tests/modules/nf-core/dedup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEDUP } from '../../../modules/dedup/main.nf' +include { DEDUP } from '../../../modules/nf-core/dedup/main.nf' workflow test_dedup { diff --git a/tests/modules/nf-core/deeparg/downloaddata/main.nf b/tests/modules/nf-core/deeparg/downloaddata/main.nf index 1074b0bcddb..523a81ffcdd 100644 --- a/tests/modules/nf-core/deeparg/downloaddata/main.nf +++ b/tests/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPARG_DOWNLOADDATA } from '../../../../modules/deeparg/downloaddata/main.nf' +include { DEEPARG_DOWNLOADDATA } from '../../../../modules/nf-core/deeparg/downloaddata/main.nf' workflow test_deeparg_downloaddata { DEEPARG_DOWNLOADDATA ( ) diff --git a/tests/modules/nf-core/deeparg/predict/main.nf b/tests/modules/nf-core/deeparg/predict/main.nf index 2ada23740e2..40247a35bb8 100644 --- a/tests/modules/nf-core/deeparg/predict/main.nf +++ b/tests/modules/nf-core/deeparg/predict/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DEEPARG_DOWNLOADDATA } from '../../../../modules/deeparg/downloaddata/main.nf' -include { DEEPARG_PREDICT } from '../../../../modules/deeparg/predict/main.nf' +include { DEEPARG_DOWNLOADDATA } from '../../../../modules/nf-core/deeparg/downloaddata/main.nf' +include { DEEPARG_PREDICT } from '../../../../modules/nf-core/deeparg/predict/main.nf' workflow test_deeparg_predict { diff --git a/tests/modules/nf-core/deepbgc/download/main.nf b/tests/modules/nf-core/deepbgc/download/main.nf index ecf3c9b6250..30094cccf14 100644 --- a/tests/modules/nf-core/deepbgc/download/main.nf +++ b/tests/modules/nf-core/deepbgc/download/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf' +include { DEEPBGC_DOWNLOAD } from '../../../../modules/nf-core/deepbgc/download/main.nf' workflow test_deepbgc_download { diff --git a/tests/modules/nf-core/deepbgc/pipeline/main.nf b/tests/modules/nf-core/deepbgc/pipeline/main.nf index a896fa51f50..a68cc33d62b 100644 --- a/tests/modules/nf-core/deepbgc/pipeline/main.nf +++ b/tests/modules/nf-core/deepbgc/pipeline/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/gunzip/main.nf' -include { PRODIGAL } from '../../../modules/prodigal/main.nf' -include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf' -include { DEEPBGC_PIPELINE } from '../../../../modules/deepbgc/pipeline/main.nf' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' +include { PRODIGAL } from '../../../modules/nf-core/prodigal/main.nf' +include { DEEPBGC_DOWNLOAD } from '../../../../modules/nf-core/deepbgc/download/main.nf' +include { DEEPBGC_PIPELINE } from '../../../../modules/nf-core/deepbgc/pipeline/main.nf' workflow test_deepbgc_pipeline_gbk { diff --git a/tests/modules/nf-core/deeptools/bamcoverage/main.nf b/tests/modules/nf-core/deeptools/bamcoverage/main.nf index 97a79508a28..202edce08db 100644 --- a/tests/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/tests/modules/nf-core/deeptools/bamcoverage/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/deeptools/bamcoverage/main.nf' +include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/nf-core/deeptools/bamcoverage/main.nf' workflow test_deeptools_bamcoverage_bam { diff --git a/tests/modules/nf-core/deeptools/computematrix/main.nf b/tests/modules/nf-core/deeptools/computematrix/main.nf index 35e49f5970b..1f9d9232a90 100644 --- a/tests/modules/nf-core/deeptools/computematrix/main.nf +++ b/tests/modules/nf-core/deeptools/computematrix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../modules/deeptools/computematrix/main.nf' +include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../modules/nf-core/deeptools/computematrix/main.nf' workflow test_deeptools_computematrix { diff --git a/tests/modules/nf-core/deeptools/plotfingerprint/main.nf b/tests/modules/nf-core/deeptools/plotfingerprint/main.nf index bcef970e966..1fe414e6e9b 100644 --- a/tests/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/tests/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -4,7 +4,7 @@ nextflow.enable.dsl = 2 params.fragment_size = 1000 -include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../modules/deeptools/plotfingerprint/main.nf' +include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../modules/nf-core/deeptools/plotfingerprint/main.nf' workflow test_deeptools_plotfingerprint { diff --git a/tests/modules/nf-core/deeptools/plotheatmap/main.nf b/tests/modules/nf-core/deeptools/plotheatmap/main.nf index 86005b2cc96..b553cbd74fb 100644 --- a/tests/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/tests/modules/nf-core/deeptools/plotheatmap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_PLOTHEATMAP } from '../../../../modules/deeptools/plotheatmap/main.nf' +include { DEEPTOOLS_PLOTHEATMAP } from '../../../../modules/nf-core/deeptools/plotheatmap/main.nf' workflow test_deeptools_plotheatmap { diff --git a/tests/modules/nf-core/deeptools/plotprofile/main.nf b/tests/modules/nf-core/deeptools/plotprofile/main.nf index 63ee47cd795..573310a4c14 100644 --- a/tests/modules/nf-core/deeptools/plotprofile/main.nf +++ b/tests/modules/nf-core/deeptools/plotprofile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_PLOTPROFILE } from '../../../../modules/deeptools/plotprofile/main.nf' +include { DEEPTOOLS_PLOTPROFILE } from '../../../../modules/nf-core/deeptools/plotprofile/main.nf' workflow test_deeptools_plotprofile { diff --git a/tests/modules/nf-core/deepvariant/main.nf b/tests/modules/nf-core/deepvariant/main.nf index 3b1b90e636c..b430ea07831 100644 --- a/tests/modules/nf-core/deepvariant/main.nf +++ b/tests/modules/nf-core/deepvariant/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DEEPVARIANT } from '../../../modules/deepvariant/main.nf' -include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/deepvariant/main.nf' +include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant/main.nf' +include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/nf-core/deepvariant/main.nf' workflow test_deepvariant { diff --git a/tests/modules/nf-core/delly/call/main.nf b/tests/modules/nf-core/delly/call/main.nf index 78dc7c37e9e..71298935676 100644 --- a/tests/modules/nf-core/delly/call/main.nf +++ b/tests/modules/nf-core/delly/call/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DELLY_CALL } from '../../../../modules/delly/call/main.nf' +include { DELLY_CALL } from '../../../../modules/nf-core/delly/call/main.nf' workflow test_delly_call_bam { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/diamond/blastp/main.nf b/tests/modules/nf-core/diamond/blastp/main.nf index ff669233d2d..c9d676e1631 100644 --- a/tests/modules/nf-core/diamond/blastp/main.nf +++ b/tests/modules/nf-core/diamond/blastp/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' -include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf' +include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_BLASTP } from '../../../../modules/nf-core/diamond/blastp/main.nf' workflow test_diamond_blastp { diff --git a/tests/modules/nf-core/diamond/blastx/main.nf b/tests/modules/nf-core/diamond/blastx/main.nf index 8316aa9172c..86d23a83597 100644 --- a/tests/modules/nf-core/diamond/blastx/main.nf +++ b/tests/modules/nf-core/diamond/blastx/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' -include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf' +include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_BLASTX } from '../../../../modules/nf-core/diamond/blastx/main.nf' workflow test_diamond_blastx { diff --git a/tests/modules/nf-core/diamond/makedb/main.nf b/tests/modules/nf-core/diamond/makedb/main.nf index d309de6d54a..30fcab92f97 100644 --- a/tests/modules/nf-core/diamond/makedb/main.nf +++ b/tests/modules/nf-core/diamond/makedb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' +include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' workflow test_diamond_makedb { diff --git a/tests/modules/nf-core/dragmap/align/main.nf b/tests/modules/nf-core/dragmap/align/main.nf index 4376602c0a8..bb4e78de7a9 100644 --- a/tests/modules/nf-core/dragmap/align/main.nf +++ b/tests/modules/nf-core/dragmap/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf' -include { DRAGMAP_ALIGN } from '../../../../modules/dragmap/align/main.nf' +include { DRAGMAP_HASHTABLE } from '../../../../modules/nf-core/dragmap/hashtable/main.nf' +include { DRAGMAP_ALIGN } from '../../../../modules/nf-core/dragmap/align/main.nf' workflow test_dragmap_align_single_end { input = [ diff --git a/tests/modules/nf-core/dragmap/hashtable/main.nf b/tests/modules/nf-core/dragmap/hashtable/main.nf index 91b43caa96c..e26d1474769 100644 --- a/tests/modules/nf-core/dragmap/hashtable/main.nf +++ b/tests/modules/nf-core/dragmap/hashtable/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf' +include { DRAGMAP_HASHTABLE } from '../../../../modules/nf-core/dragmap/hashtable/main.nf' workflow test_dragmap_hashtable { diff --git a/tests/modules/nf-core/dragonflye/main.nf b/tests/modules/nf-core/dragonflye/main.nf index 3d59bb21ebd..2073a41fec7 100644 --- a/tests/modules/nf-core/dragonflye/main.nf +++ b/tests/modules/nf-core/dragonflye/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DRAGONFLYE } from '../../../modules/dragonflye/main.nf' -include { DRAGONFLYE as DRAGONFLYE_RAVEN } from '../../../modules/dragonflye/main.nf' +include { DRAGONFLYE } from '../../../modules/nf-core/dragonflye/main.nf' +include { DRAGONFLYE as DRAGONFLYE_RAVEN } from '../../../modules/nf-core/dragonflye/main.nf' workflow test_dragonflye { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/dshbio/exportsegments/main.nf b/tests/modules/nf-core/dshbio/exportsegments/main.nf index 0460950af99..c4447dc1ae3 100644 --- a/tests/modules/nf-core/dshbio/exportsegments/main.nf +++ b/tests/modules/nf-core/dshbio/exportsegments/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_EXPORTSEGMENTS } from '../../../../modules/dshbio/exportsegments/main.nf' +include { DSHBIO_EXPORTSEGMENTS } from '../../../../modules/nf-core/dshbio/exportsegments/main.nf' workflow test_dshbio_exportsegments { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/filterbed/main.nf b/tests/modules/nf-core/dshbio/filterbed/main.nf index 454a03be3d4..e4efaaa7057 100644 --- a/tests/modules/nf-core/dshbio/filterbed/main.nf +++ b/tests/modules/nf-core/dshbio/filterbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_FILTERBED } from '../../../../modules/dshbio/filterbed/main.nf' +include { DSHBIO_FILTERBED } from '../../../../modules/nf-core/dshbio/filterbed/main.nf' workflow test_dshbio_filterbed { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/filtergff3/main.nf b/tests/modules/nf-core/dshbio/filtergff3/main.nf index 7c803781cac..1337c030f3c 100644 --- a/tests/modules/nf-core/dshbio/filtergff3/main.nf +++ b/tests/modules/nf-core/dshbio/filtergff3/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_FILTERGFF3 } from '../../../../modules/dshbio/filtergff3/main.nf' +include { DSHBIO_FILTERGFF3 } from '../../../../modules/nf-core/dshbio/filtergff3/main.nf' workflow test_dshbio_filtergff3 { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/splitbed/main.nf b/tests/modules/nf-core/dshbio/splitbed/main.nf index 517baad0ed4..e70c5235534 100644 --- a/tests/modules/nf-core/dshbio/splitbed/main.nf +++ b/tests/modules/nf-core/dshbio/splitbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_SPLITBED } from '../../../../modules/dshbio/splitbed/main.nf' +include { DSHBIO_SPLITBED } from '../../../../modules/nf-core/dshbio/splitbed/main.nf' workflow test_dshbio_splitbed { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/splitgff3/main.nf b/tests/modules/nf-core/dshbio/splitgff3/main.nf index 03aa53947bf..e9f9f302585 100644 --- a/tests/modules/nf-core/dshbio/splitgff3/main.nf +++ b/tests/modules/nf-core/dshbio/splitgff3/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_SPLITGFF3 } from '../../../../modules/dshbio/splitgff3/main.nf' +include { DSHBIO_SPLITGFF3 } from '../../../../modules/nf-core/dshbio/splitgff3/main.nf' workflow test_dshbio_splitgff3 { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/ectyper/main.nf b/tests/modules/nf-core/ectyper/main.nf index dd359fa23d3..3279d8358d7 100644 --- a/tests/modules/nf-core/ectyper/main.nf +++ b/tests/modules/nf-core/ectyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ECTYPER } from '../../../modules/ectyper/main.nf' +include { ECTYPER } from '../../../modules/nf-core/ectyper/main.nf' workflow test_ectyper { diff --git a/tests/modules/nf-core/eido/convert/main.nf b/tests/modules/nf-core/eido/convert/main.nf index e3e49771be2..2eb26b4c4c1 100644 --- a/tests/modules/nf-core/eido/convert/main.nf +++ b/tests/modules/nf-core/eido/convert/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EIDO_CONVERT } from '../../../../modules/eido/convert/main.nf' +include { EIDO_CONVERT } from '../../../../modules/nf-core/eido/convert/main.nf' workflow test_eido_convert_nextflow_samplesheet { diff --git a/tests/modules/nf-core/eido/validate/main.nf b/tests/modules/nf-core/eido/validate/main.nf index d1e2d200430..24400e9304d 100644 --- a/tests/modules/nf-core/eido/validate/main.nf +++ b/tests/modules/nf-core/eido/validate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EIDO_VALIDATE } from '../../../../modules/eido/validate/main.nf' +include { EIDO_VALIDATE } from '../../../../modules/nf-core/eido/validate/main.nf' workflow test_eido_validate_on_nextflow_samplesheet { diff --git a/tests/modules/nf-core/elprep/filter/main.nf b/tests/modules/nf-core/elprep/filter/main.nf index 0a8d43ca234..72bc27fe45a 100644 --- a/tests/modules/nf-core/elprep/filter/main.nf +++ b/tests/modules/nf-core/elprep/filter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ELPREP_FILTER } from '../../../../modules/elprep/filter/main.nf' +include { ELPREP_FILTER } from '../../../../modules/nf-core/elprep/filter/main.nf' workflow test_elprep_filter { diff --git a/tests/modules/nf-core/elprep/merge/main.nf b/tests/modules/nf-core/elprep/merge/main.nf index b4a40ce3fc5..7f74d38f723 100644 --- a/tests/modules/nf-core/elprep/merge/main.nf +++ b/tests/modules/nf-core/elprep/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf' -include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf' +include { ELPREP_SPLIT } from '../../../../modules/nf-core/elprep/split/main.nf' +include { ELPREP_MERGE } from '../../../../modules/nf-core/elprep/merge/main.nf' workflow test_elprep_merge { diff --git a/tests/modules/nf-core/elprep/split/main.nf b/tests/modules/nf-core/elprep/split/main.nf index d5a111de8f3..de98c390f3c 100644 --- a/tests/modules/nf-core/elprep/split/main.nf +++ b/tests/modules/nf-core/elprep/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf' +include { ELPREP_SPLIT } from '../../../../modules/nf-core/elprep/split/main.nf' workflow test_elprep_split { diff --git a/tests/modules/nf-core/emboss/seqret/main.nf b/tests/modules/nf-core/emboss/seqret/main.nf index d3c703a2ac3..bc9193f76f8 100644 --- a/tests/modules/nf-core/emboss/seqret/main.nf +++ b/tests/modules/nf-core/emboss/seqret/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { EMBOSS_SEQRET } from '../../../../modules/emboss/seqret/main.nf' -include { GUNZIP } from '../../../modules/gunzip/main.nf' +include { EMBOSS_SEQRET } from '../../../../modules/nf-core/emboss/seqret/main.nf' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' workflow test_emboss_seqret_gb2embl { diff --git a/tests/modules/nf-core/emmtyper/main.nf b/tests/modules/nf-core/emmtyper/main.nf index ee96fc322f2..68bd23dda35 100644 --- a/tests/modules/nf-core/emmtyper/main.nf +++ b/tests/modules/nf-core/emmtyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EMMTYPER } from '../../../modules/emmtyper/main.nf' +include { EMMTYPER } from '../../../modules/nf-core/emmtyper/main.nf' workflow test_emmtyper { diff --git a/tests/modules/nf-core/endorspy/main.nf b/tests/modules/nf-core/endorspy/main.nf index 2f04c13a47d..63cedef11bd 100644 --- a/tests/modules/nf-core/endorspy/main.nf +++ b/tests/modules/nf-core/endorspy/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { ENDORSPY } from '../../../modules/endorspy/main.nf' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main.nf' -include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../modules/samtools/flagstat/main.nf' -include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf' -include { SAMTOOLS_INDEX } from '../../../modules/samtools/index/main.nf' +include { ENDORSPY } from '../../../modules/nf-core/endorspy/main.nf' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main.nf' +include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../modules/nf-core/samtools/flagstat/main.nf' +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main.nf' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main.nf' workflow test_endorspy { diff --git a/tests/modules/nf-core/ensemblvep/main.nf b/tests/modules/nf-core/ensemblvep/main.nf index 8854d1a28c5..88d63232bfa 100644 --- a/tests/modules/nf-core/ensemblvep/main.nf +++ b/tests/modules/nf-core/ensemblvep/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf' +include { ENSEMBLVEP } from '../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../modules/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } from '../../../modules/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } from '../../../modules/nf-core/ensemblvep/main.nf' workflow test_ensemblvep_fasta_json { input = [ diff --git a/tests/modules/nf-core/entrezdirect/esummary/main.nf b/tests/modules/nf-core/entrezdirect/esummary/main.nf index 8308102cbfb..f86f7c77544 100644 --- a/tests/modules/nf-core/entrezdirect/esummary/main.nf +++ b/tests/modules/nf-core/entrezdirect/esummary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/entrezdirect/esummary/main.nf' +include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/nf-core/entrezdirect/esummary/main.nf' // // Test with SRA database diff --git a/tests/modules/nf-core/entrezdirect/xtract/main.nf b/tests/modules/nf-core/entrezdirect/xtract/main.nf index 93cd38491ba..934fc2e6e62 100644 --- a/tests/modules/nf-core/entrezdirect/xtract/main.nf +++ b/tests/modules/nf-core/entrezdirect/xtract/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/entrezdirect/esummary/main.nf' -include { ENTREZDIRECT_XTRACT } from '../../../../modules/entrezdirect/xtract/main.nf' +include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/nf-core/entrezdirect/esummary/main.nf' +include { ENTREZDIRECT_XTRACT } from '../../../../modules/nf-core/entrezdirect/xtract/main.nf' // // Test with Assembly database diff --git a/tests/modules/nf-core/epang/main.nf b/tests/modules/nf-core/epang/main.nf index d2c64ad8bda..5496ffe4047 100644 --- a/tests/modules/nf-core/epang/main.nf +++ b/tests/modules/nf-core/epang/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EPANG } from '../../../modules/epang/main.nf' +include { EPANG } from '../../../modules/nf-core/epang/main.nf' workflow test_epang { diff --git a/tests/modules/nf-core/expansionhunter/main.nf b/tests/modules/nf-core/expansionhunter/main.nf index d0221234b97..1f5a41edeab 100644 --- a/tests/modules/nf-core/expansionhunter/main.nf +++ b/tests/modules/nf-core/expansionhunter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf' +include { EXPANSIONHUNTER } from '../../../modules/nf-core/expansionhunter/main.nf' workflow test_expansionhunter { diff --git a/tests/modules/nf-core/faqcs/main.nf b/tests/modules/nf-core/faqcs/main.nf index eba4bb97206..06e12c5de45 100644 --- a/tests/modules/nf-core/faqcs/main.nf +++ b/tests/modules/nf-core/faqcs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FAQCS } from '../../../modules/faqcs/main.nf' +include { FAQCS } from '../../../modules/nf-core/faqcs/main.nf' // diff --git a/tests/modules/nf-core/fargene/main.nf b/tests/modules/nf-core/fargene/main.nf index 471862e17e0..aecdbf67254 100644 --- a/tests/modules/nf-core/fargene/main.nf +++ b/tests/modules/nf-core/fargene/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/gunzip/main.nf' -include { FARGENE } from '../../../modules/fargene/main.nf' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' +include { FARGENE } from '../../../modules/nf-core/fargene/main.nf' workflow test_fargene { diff --git a/tests/modules/nf-core/fastani/main.nf b/tests/modules/nf-core/fastani/main.nf index 0395f6a9b94..bb20fa296d4 100644 --- a/tests/modules/nf-core/fastani/main.nf +++ b/tests/modules/nf-core/fastani/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTANI } from '../../../modules/fastani/main.nf' +include { FASTANI } from '../../../modules/nf-core/fastani/main.nf' workflow test_fastani { diff --git a/tests/modules/nf-core/fastawindows/main.nf b/tests/modules/nf-core/fastawindows/main.nf index 28d367d98bc..8abccb01b65 100644 --- a/tests/modules/nf-core/fastawindows/main.nf +++ b/tests/modules/nf-core/fastawindows/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTAWINDOWS } from '../../../modules/fastawindows/main.nf' +include { FASTAWINDOWS } from '../../../modules/nf-core/fastawindows/main.nf' workflow test_fastawindows { diff --git a/tests/modules/nf-core/fastk/fastk/main.nf b/tests/modules/nf-core/fastk/fastk/main.nf index 944d434f415..e00102f92cd 100644 --- a/tests/modules/nf-core/fastk/fastk/main.nf +++ b/tests/modules/nf-core/fastk/fastk/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' workflow test_fastk_fastk_single_end { diff --git a/tests/modules/nf-core/fastk/histex/main.nf b/tests/modules/nf-core/fastk/histex/main.nf index 74b46378181..c4656df5879 100644 --- a/tests/modules/nf-core/fastk/histex/main.nf +++ b/tests/modules/nf-core/fastk/histex/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf' -include { FASTK_HISTEX } from '../../../../modules/fastk/histex/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_HISTEX } from '../../../../modules/nf-core/fastk/histex/main.nf' workflow test_fastk_histex { diff --git a/tests/modules/nf-core/fastk/merge/main.nf b/tests/modules/nf-core/fastk/merge/main.nf index 1bed019e4fc..abccfc74507 100644 --- a/tests/modules/nf-core/fastk/merge/main.nf +++ b/tests/modules/nf-core/fastk/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf' -include { FASTK_MERGE } from '../../../../modules/fastk/merge/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_MERGE } from '../../../../modules/nf-core/fastk/merge/main.nf' workflow test_fastk_merge_hist_only { diff --git a/tests/modules/nf-core/fastp/main.nf b/tests/modules/nf-core/fastp/main.nf index 5073673a160..e5fa3badf45 100644 --- a/tests/modules/nf-core/fastp/main.nf +++ b/tests/modules/nf-core/fastp/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTP } from '../../../modules/fastp/main.nf' +include { FASTP } from '../../../modules/nf-core/fastp/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/fastqc/main.nf b/tests/modules/nf-core/fastqc/main.nf index f7db9b7cc41..fc13cb97a1f 100644 --- a/tests/modules/nf-core/fastqc/main.nf +++ b/tests/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTQC } from '../../../modules/fastqc/main.nf' +include { FASTQC } from '../../../modules/nf-core/fastqc/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/fastqscan/main.nf b/tests/modules/nf-core/fastqscan/main.nf index b9a321fe4b0..d5b517a6bdc 100644 --- a/tests/modules/nf-core/fastqscan/main.nf +++ b/tests/modules/nf-core/fastqscan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTQSCAN } from '../../../modules/fastqscan/main.nf' +include { FASTQSCAN } from '../../../modules/nf-core/fastqscan/main.nf' workflow test_fastqscan { diff --git a/tests/modules/nf-core/fasttree/main.nf b/tests/modules/nf-core/fasttree/main.nf index e33228a90a8..c61a56df07d 100644 --- a/tests/modules/nf-core/fasttree/main.nf +++ b/tests/modules/nf-core/fasttree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTTREE } from '../../../modules/fasttree/main.nf' +include { FASTTREE } from '../../../modules/nf-core/fasttree/main.nf' workflow test_fasttree { diff --git a/tests/modules/nf-core/fcs/fcsadaptor/main.nf b/tests/modules/nf-core/fcs/fcsadaptor/main.nf index f86dd4301dc..1101e5c8731 100644 --- a/tests/modules/nf-core/fcs/fcsadaptor/main.nf +++ b/tests/modules/nf-core/fcs/fcsadaptor/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FCS_FCSADAPTOR } from '../../../../modules/fcs/fcsadaptor/main.nf' +include { FCS_FCSADAPTOR } from '../../../../modules/nf-core/fcs/fcsadaptor/main.nf' workflow test_fcs_fcsadaptor { diff --git a/tests/modules/nf-core/ffq/main.nf b/tests/modules/nf-core/ffq/main.nf index 271e9afb201..92725f7a5fd 100644 --- a/tests/modules/nf-core/ffq/main.nf +++ b/tests/modules/nf-core/ffq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FFQ } from '../../../modules/ffq/main.nf' +include { FFQ } from '../../../modules/nf-core/ffq/main.nf' workflow test_ffq_single_id { diff --git a/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index e31fdf39761..af06b72091d 100644 --- a/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf' -include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../modules/fgbio/callmolecularconsensusreads/main.nf' +include { FGBIO_SORTBAM } from '../../../../modules/nf-core/fgbio/sortbam/main.nf' +include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf' workflow test_fgbio_callmolecularconsensusreads { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/fgbio/fastqtobam/main.nf b/tests/modules/nf-core/fgbio/fastqtobam/main.nf index 794e66aafcd..b50eb2d91b6 100644 --- a/tests/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/tests/modules/nf-core/fgbio/fastqtobam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf' +include { FGBIO_FASTQTOBAM } from '../../../../modules/nf-core/fgbio/fastqtobam/main.nf' workflow test_fgbio_fastqtobam_paired_default { diff --git a/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf index b9bb350aa49..d992a1a0347 100644 --- a/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/fgbio/groupreadsbyumi/main.nf' +include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/nf-core/fgbio/groupreadsbyumi/main.nf' workflow test_fgbio_groupreadsbyumi { diff --git a/tests/modules/nf-core/fgbio/sortbam/main.nf b/tests/modules/nf-core/fgbio/sortbam/main.nf index ada99d0f1da..d153d819961 100644 --- a/tests/modules/nf-core/fgbio/sortbam/main.nf +++ b/tests/modules/nf-core/fgbio/sortbam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf' +include { FGBIO_SORTBAM } from '../../../../modules/nf-core/fgbio/sortbam/main.nf' workflow test_fgbio_sortbam { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/filtlong/main.nf b/tests/modules/nf-core/filtlong/main.nf index df7892aa04f..0499278a487 100644 --- a/tests/modules/nf-core/filtlong/main.nf +++ b/tests/modules/nf-core/filtlong/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FILTLONG } from '../../../modules/filtlong/main.nf' +include { FILTLONG } from '../../../modules/nf-core/filtlong/main.nf' workflow test_filtlong { diff --git a/tests/modules/nf-core/flash/main.nf b/tests/modules/nf-core/flash/main.nf index 4afcb8fcb24..5d183e9d0bc 100644 --- a/tests/modules/nf-core/flash/main.nf +++ b/tests/modules/nf-core/flash/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FLASH } from '../../../modules/flash/main.nf' +include { FLASH } from '../../../modules/nf-core/flash/main.nf' workflow test_flash { input = [ diff --git a/tests/modules/nf-core/flye/main.nf b/tests/modules/nf-core/flye/main.nf index c078c4da52e..6fef10bec2a 100644 --- a/tests/modules/nf-core/flye/main.nf +++ b/tests/modules/nf-core/flye/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FLYE } from '../../../modules/flye/main.nf' +include { FLYE } from '../../../modules/nf-core/flye/main.nf' workflow test_flye_pacbio_raw { diff --git a/tests/modules/nf-core/fq/lint/main.nf b/tests/modules/nf-core/fq/lint/main.nf index 677d32f7fb9..91c6350b151 100644 --- a/tests/modules/nf-core/fq/lint/main.nf +++ b/tests/modules/nf-core/fq/lint/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FQ_LINT } from '../../../../modules/fq/lint/main.nf' +include { FQ_LINT } from '../../../../modules/nf-core/fq/lint/main.nf' workflow test_fq_lint_success { diff --git a/tests/modules/nf-core/freebayes/main.nf b/tests/modules/nf-core/freebayes/main.nf index 6ed708c5f82..472b00d2d91 100644 --- a/tests/modules/nf-core/freebayes/main.nf +++ b/tests/modules/nf-core/freebayes/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FREEBAYES } from '../../../modules/freebayes/main.nf' +include { FREEBAYES } from '../../../modules/nf-core/freebayes/main.nf' workflow test_freebayes { targets = [] diff --git a/tests/modules/nf-core/gamma/gamma/main.nf b/tests/modules/nf-core/gamma/gamma/main.nf index 97e58be7e05..2e90bb437c0 100644 --- a/tests/modules/nf-core/gamma/gamma/main.nf +++ b/tests/modules/nf-core/gamma/gamma/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf' +include { GAMMA_GAMMA } from '../../../../modules/nf-core/gamma/gamma/main.nf' workflow test_unzip { diff --git a/tests/modules/nf-core/gappa/examineassign/main.nf b/tests/modules/nf-core/gappa/examineassign/main.nf index c42a2033d61..e93135274e1 100644 --- a/tests/modules/nf-core/gappa/examineassign/main.nf +++ b/tests/modules/nf-core/gappa/examineassign/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAPPA_EXAMINEASSIGN } from '../../../../modules/gappa/examineassign/main.nf' +include { GAPPA_EXAMINEASSIGN } from '../../../../modules/nf-core/gappa/examineassign/main.nf' workflow test_gappa_examineassign { diff --git a/tests/modules/nf-core/gappa/examinegraft/main.nf b/tests/modules/nf-core/gappa/examinegraft/main.nf index f137a32e90d..ea86db6d905 100644 --- a/tests/modules/nf-core/gappa/examinegraft/main.nf +++ b/tests/modules/nf-core/gappa/examinegraft/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAPPA_EXAMINEGRAFT } from '../../../../modules/gappa/examinegraft/main.nf' +include { GAPPA_EXAMINEGRAFT } from '../../../../modules/nf-core/gappa/examinegraft/main.nf' workflow test_gappa_examinegraft { diff --git a/tests/modules/nf-core/gappa/examineheattree/main.nf b/tests/modules/nf-core/gappa/examineheattree/main.nf index bee1449252b..bc5a3d6a3e0 100644 --- a/tests/modules/nf-core/gappa/examineheattree/main.nf +++ b/tests/modules/nf-core/gappa/examineheattree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAPPA_EXAMINEHEATTREE } from '../../../../modules/gappa/examineheattree/main.nf' +include { GAPPA_EXAMINEHEATTREE } from '../../../../modules/nf-core/gappa/examineheattree/main.nf' workflow test_gappa_examineheattree { diff --git a/tests/modules/nf-core/gatk/indelrealigner/main.nf b/tests/modules/nf-core/gatk/indelrealigner/main.nf index d4e01e128ff..9190d0f2a7b 100644 --- a/tests/modules/nf-core/gatk/indelrealigner/main.nf +++ b/tests/modules/nf-core/gatk/indelrealigner/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf' -include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf' +include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/nf-core/gatk/realignertargetcreator/main.nf' +include { GATK_INDELREALIGNER } from '../../../../modules/nf-core/gatk/indelrealigner/main.nf' workflow test_gatk_indelrealigner { diff --git a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf index 4b9f8effa74..1193f297707 100644 --- a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf' +include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/nf-core/gatk/realignertargetcreator/main.nf' workflow test_gatk_realignertargetcreator { diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf index 6d145e76073..f349ae67d8b 100644 --- a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/gatk/unifiedgenotyper/main.nf' +include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' workflow test_gatk_unifiedgenotyper { diff --git a/tests/modules/nf-core/gatk4/applybqsr/main.nf b/tests/modules/nf-core/gatk4/applybqsr/main.nf index 66711574780..dc7284776aa 100644 --- a/tests/modules/nf-core/gatk4/applybqsr/main.nf +++ b/tests/modules/nf-core/gatk4/applybqsr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf' +include { GATK4_APPLYBQSR } from '../../../../modules/nf-core/gatk4/applybqsr/main.nf' workflow test_gatk4_applybqsr { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/main.nf b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf index ee1f88dddfe..32f0b72dacf 100644 --- a/tests/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYBQSR_SPARK } from '../../../../modules/gatk4/applybqsrspark/main.nf' +include { GATK4_APPLYBQSR_SPARK } from '../../../../modules/nf-core/gatk4/applybqsrspark/main.nf' workflow test_gatk4_applybqsr_spark { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/applyvqsr/main.nf b/tests/modules/nf-core/gatk4/applyvqsr/main.nf index c6e99d5c063..355b86e2871 100644 --- a/tests/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/tests/modules/nf-core/gatk4/applyvqsr/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/gatk4/applyvqsr/main.nf' -include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/nf-core/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/nf-core/gatk4/applyvqsr/main.nf' workflow test_gatk4_applyvqsr { input = [ [ id:'test'], // meta map diff --git a/tests/modules/nf-core/gatk4/baserecalibrator/main.nf b/tests/modules/nf-core/gatk4/baserecalibrator/main.nf index 05c24ae319a..19df0d65001 100644 --- a/tests/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/tests/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_BASERECALIBRATOR } from '../../../../modules/gatk4/baserecalibrator/main.nf' +include { GATK4_BASERECALIBRATOR } from '../../../../modules/nf-core/gatk4/baserecalibrator/main.nf' workflow test_gatk4_baserecalibrator { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf index 8419e16b724..e1d03c47d44 100644 --- a/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_BASERECALIBRATOR_SPARK } from '../../../../modules/gatk4/baserecalibratorspark/main.nf' +include { GATK4_BASERECALIBRATOR_SPARK } from '../../../../modules/nf-core/gatk4/baserecalibratorspark/main.nf' workflow test_gatk4_baserecalibrator_spark { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/main.nf b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf index 2dd72904f72..c2414d4f1f6 100644 --- a/tests/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf' +include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' workflow test_gatk4_bedtointervallist { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/main.nf b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf index c6e085b1e5a..a4ff1099e3b 100644 --- a/tests/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/gatk4/calculatecontamination/main.nf' -include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../modules/gatk4/calculatecontamination/main.nf' +include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/nf-core/gatk4/calculatecontamination/main.nf' +include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../modules/nf-core/gatk4/calculatecontamination/main.nf' workflow test_gatk4_calculatecontamination_tumor_only { diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 136a9742ce3..54f7b44e7b9 100644 --- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../modules/gatk4/calibratedragstrmodel/main.nf' +include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../modules/nf-core/gatk4/calibratedragstrmodel/main.nf' workflow test_gatk4_calibratedragstrmodel_bam { diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf index 1654c54a8e3..c9b570dbac6 100644 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf' +include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' workflow test_gatk4_cnnscorevariants { diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf index 9e69c018f45..08dfb5b1570 100644 --- a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COLLECTREADCOUNTS } from '../../../../modules/gatk4/collectreadcounts/main.nf' +include { GATK4_COLLECTREADCOUNTS } from '../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' workflow test_gatk4_collectreadcounts_hdf5 { diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf index 21761d6a870..277fc7215c3 100644 --- a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/gatk4/collectsvevidence/main.nf' +include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' workflow test_gatk4_collectsvevidence_cram { diff --git a/tests/modules/nf-core/gatk4/combinegvcfs/main.nf b/tests/modules/nf-core/gatk4/combinegvcfs/main.nf index 50d42625168..a518e050e50 100644 --- a/tests/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/tests/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COMBINEGVCFS } from '../../../../modules/gatk4/combinegvcfs/main.nf' +include { GATK4_COMBINEGVCFS } from '../../../../modules/nf-core/gatk4/combinegvcfs/main.nf' workflow test_gatk4_combinegvcfs { diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf index 8fccadb9dc3..e35032b7784 100644 --- a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestrtablefile/main.nf' +include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/nf-core/gatk4/composestrtablefile/main.nf' workflow test_gatk4_composestrtablefile { diff --git a/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf b/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf index b304b0432a8..5398588422e 100644 --- a/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../modules/gatk4/createsequencedictionary/main.nf' +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../modules/nf-core/gatk4/createsequencedictionary/main.nf' workflow test_gatk4_createsequencedictionary { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 3316f73ac95..df266647ca3 100644 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/gatk4/createsomaticpanelofnormals/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf' workflow test_gatk4_createsomaticpanelofnormals { db = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index 398a6c7997e..d3458a904b2 100644 --- a/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/gatk4/estimatelibrarycomplexity/main.nf' +include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf' workflow test_gatk4_estimatelibrarycomplexity { diff --git a/tests/modules/nf-core/gatk4/fastqtosam/main.nf b/tests/modules/nf-core/gatk4/fastqtosam/main.nf index 4f53c791101..77a12aef9b0 100644 --- a/tests/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/tests/modules/nf-core/gatk4/fastqtosam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_FASTQTOSAM } from '../../../../modules/gatk4/fastqtosam/main.nf' +include { GATK4_FASTQTOSAM } from '../../../../modules/nf-core/gatk4/fastqtosam/main.nf' workflow test_gatk4_fastqtosam_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf b/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf index 1a4ee377d22..da3e573fddc 100644 --- a/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutectcalls/main.nf' +include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/nf-core/gatk4/filtermutectcalls/main.nf' workflow test_gatk4_filtermutectcalls_base { diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf index 91dde3d425c..bfb4e20ab54 100644 --- a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf' -include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf' -include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf' +include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/nf-core/gatk4/filtervarianttranches/main.nf' +include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' +include { GATK4_HAPLOTYPECALLER } from '../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' workflow test_gatk4_filtervarianttranches { resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 2693a06a0df..586008a5b1c 100644 --- a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_GATHERBQSRREPORTS } from '../../../../modules/gatk4/gatherbqsrreports/main.nf' +include { GATK4_GATHERBQSRREPORTS } from '../../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf' workflow test_gatk4_gatherbqsrreports { diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index 2bd7e98c4d0..afe8dc39477 100644 --- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../modules/gatk4/gatherpileupsummaries/main.nf' +include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../modules/nf-core/gatk4/gatherpileupsummaries/main.nf' workflow test_gatk4_gatherpileupsummaries { diff --git a/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf b/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf index 6d990f4e94a..01fda733d2e 100644 --- a/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { GATK4_GENOMICSDBIMPORT } from '../../../../modules/gatk4/genomicsdbimport/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { GATK4_GENOMICSDBIMPORT } from '../../../../modules/nf-core/gatk4/genomicsdbimport/main.nf' workflow test_gatk4_genomicsdbimport_create_genomicsdb { diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf index cd7d3a03c25..b9b9a68a8bb 100644 --- a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_GENOTYPEGVCFS } from '../../../../modules/gatk4/genotypegvcfs/main.nf' -include { UNTAR } from '../../../../modules/untar/main.nf' +include { GATK4_GENOTYPEGVCFS } from '../../../../modules/nf-core/gatk4/genotypegvcfs/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' // Basic parameters with uncompressed VCF input workflow test_gatk4_genotypegvcfs_vcf_input { diff --git a/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf index 2a53e35e284..898d0e3b8b2 100644 --- a/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf' +include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/nf-core/gatk4/getpileupsummaries/main.nf' workflow test_gatk4_getpileupsummaries_separate_sites { diff --git a/tests/modules/nf-core/gatk4/haplotypecaller/main.nf b/tests/modules/nf-core/gatk4/haplotypecaller/main.nf index 3ad3dfb5deb..adee2d1a069 100644 --- a/tests/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/tests/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf' +include { GATK4_HAPLOTYPECALLER } from '../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' workflow test_gatk4_haplotypecaller { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf b/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf index f61b57fc532..9e718295022 100644 --- a/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_INDEXFEATUREFILE } from '../../../../modules/gatk4/indexfeaturefile/main.nf' +include { GATK4_INDEXFEATUREFILE } from '../../../../modules/nf-core/gatk4/indexfeaturefile/main.nf' workflow test_gatk4_indexfeaturefile_bed { diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf index 2963979fd3a..81988b0bad8 100644 --- a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_INTERVALLISTTOBED } from '../../../../modules/gatk4/intervallisttobed/main.nf' +include { GATK4_INTERVALLISTTOBED } from '../../../../modules/nf-core/gatk4/intervallisttobed/main.nf' workflow test_gatk4_intervallisttobed { diff --git a/tests/modules/nf-core/gatk4/intervallisttools/main.nf b/tests/modules/nf-core/gatk4/intervallisttools/main.nf index 535923fbafb..0239edbdf5f 100644 --- a/tests/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/tests/modules/nf-core/gatk4/intervallisttools/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf' -include { GATK4_INTERVALLISTTOOLS } from '../../../../modules/gatk4/intervallisttools/main.nf' +include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' +include { GATK4_INTERVALLISTTOOLS } from '../../../../modules/nf-core/gatk4/intervallisttools/main.nf' workflow test_gatk4_intervallisttools { diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index dc6e8b89b5a..efdf1e83262 100644 --- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/gatk4/learnreadorientationmodel/main.nf' +include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/nf-core/gatk4/learnreadorientationmodel/main.nf' workflow test_gatk4_learnreadorientationmodel { diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 1d890a54458..192872cdb42 100644 --- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/gatk4/leftalignandtrimvariants/main.nf' +include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/nf-core/gatk4/leftalignandtrimvariants/main.nf' workflow test_gatk4_leftalignandtrimvariants_interval { diff --git a/tests/modules/nf-core/gatk4/markduplicates/main.nf b/tests/modules/nf-core/gatk4/markduplicates/main.nf index e5ece314c3d..c76813c3e36 100644 --- a/tests/modules/nf-core/gatk4/markduplicates/main.nf +++ b/tests/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf' -include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/gatk4/markduplicates/main.nf' +include { GATK4_MARKDUPLICATES } from '../../../../modules/nf-core/gatk4/markduplicates/main.nf' +include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/nf-core/gatk4/markduplicates/main.nf' workflow test_gatk4_markduplicates { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf b/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf index 004fbb1e3f1..64e4261bcda 100644 --- a/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf' -include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf' -include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf' +include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' +include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' +include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' workflow test_gatk4_markduplicates_spark { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf index d0949a523cf..da2fc14444a 100644 --- a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf' +include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/nf-core/gatk4/mergebamalignment/main.nf' workflow test_gatk4_mergebamalignment { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/mergemutectstats/main.nf b/tests/modules/nf-core/gatk4/mergemutectstats/main.nf index bf65a6a67e3..522f48c2142 100644 --- a/tests/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/tests/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_MERGEMUTECTSTATS } from '../../../../modules/gatk4/mergemutectstats/main.nf' +include { GATK4_MERGEMUTECTSTATS } from '../../../../modules/nf-core/gatk4/mergemutectstats/main.nf' workflow test_gatk4_mergemutectstats { diff --git a/tests/modules/nf-core/gatk4/mergevcfs/main.nf b/tests/modules/nf-core/gatk4/mergevcfs/main.nf index 32569bdf46b..e10575e9429 100644 --- a/tests/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/tests/modules/nf-core/gatk4/mergevcfs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_MERGEVCFS } from '../../../../modules/gatk4/mergevcfs/main.nf' +include { GATK4_MERGEVCFS } from '../../../../modules/nf-core/gatk4/mergevcfs/main.nf' workflow test_gatk4_mergevcfs { def input = [] diff --git a/tests/modules/nf-core/gatk4/mutect2/main.nf b/tests/modules/nf-core/gatk4/mutect2/main.nf index fa229effd4e..6385c51dfec 100644 --- a/tests/modules/nf-core/gatk4/mutect2/main.nf +++ b/tests/modules/nf-core/gatk4/mutect2/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GATK4_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf' -include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../modules/gatk4/mutect2/main.nf' -include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../modules/gatk4/mutect2/main.nf' -include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../modules/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' workflow test_gatk4_mutect2_tumor_normal_pair { input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map diff --git a/tests/modules/nf-core/gatk4/printsvevidence/main.nf b/tests/modules/nf-core/gatk4/printsvevidence/main.nf index 17a4d99ee1a..2389046e770 100644 --- a/tests/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/tests/modules/nf-core/gatk4/printsvevidence/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../modules/gatk4/printsvevidence/main.nf' -include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../modules/gatk4/printsvevidence/main.nf' -include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/gatk4/collectsvevidence/main.nf' +include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../modules/nf-core/gatk4/printsvevidence/main.nf' +include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../modules/nf-core/gatk4/printsvevidence/main.nf' +include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' workflow test_gatk4_printsvevidence { diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/main.nf b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf index 2233a5c571a..5e8c7dc7780 100644 --- a/tests/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_REBLOCKGVCF } from '../../../../modules/gatk4/reblockgvcf/main.nf' +include { GATK4_REBLOCKGVCF } from '../../../../modules/nf-core/gatk4/reblockgvcf/main.nf' workflow test_gatk4_reblockgvcf { diff --git a/tests/modules/nf-core/gatk4/revertsam/main.nf b/tests/modules/nf-core/gatk4/revertsam/main.nf index 5b14d471920..3a6a8ad3e10 100644 --- a/tests/modules/nf-core/gatk4/revertsam/main.nf +++ b/tests/modules/nf-core/gatk4/revertsam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_REVERTSAM } from '../../../../modules/gatk4/revertsam/main.nf' +include { GATK4_REVERTSAM } from '../../../../modules/nf-core/gatk4/revertsam/main.nf' workflow test_gatk4_revertsam { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/samtofastq/main.nf b/tests/modules/nf-core/gatk4/samtofastq/main.nf index 757b080fd1d..6ec4b4c8194 100644 --- a/tests/modules/nf-core/gatk4/samtofastq/main.nf +++ b/tests/modules/nf-core/gatk4/samtofastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SAMTOFASTQ } from '../../../../modules/gatk4/samtofastq/main.nf' +include { GATK4_SAMTOFASTQ } from '../../../../modules/nf-core/gatk4/samtofastq/main.nf' workflow test_gatk4_samtofastq_single_end { input = [ [ id:'test', single_end: true ], // meta map diff --git a/tests/modules/nf-core/gatk4/selectvariants/main.nf b/tests/modules/nf-core/gatk4/selectvariants/main.nf index 7005dcd363e..047ef8def10 100644 --- a/tests/modules/nf-core/gatk4/selectvariants/main.nf +++ b/tests/modules/nf-core/gatk4/selectvariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SELECTVARIANTS } from '../../../../modules/gatk4/selectvariants/main.nf' +include { GATK4_SELECTVARIANTS } from '../../../../modules/nf-core/gatk4/selectvariants/main.nf' // Basic parameters with uncompressed VCF input workflow test_gatk4_selectvariants_vcf_input { diff --git a/tests/modules/nf-core/gatk4/splitintervals/main.nf b/tests/modules/nf-core/gatk4/splitintervals/main.nf index f507ece5039..7c73ee18f32 100644 --- a/tests/modules/nf-core/gatk4/splitintervals/main.nf +++ b/tests/modules/nf-core/gatk4/splitintervals/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SPLITINTERVALS } from '../../../../modules/gatk4/splitintervals/main.nf' +include { GATK4_SPLITINTERVALS } from '../../../../modules/nf-core/gatk4/splitintervals/main.nf' workflow test_gatk4_splitintervals_bed { diff --git a/tests/modules/nf-core/gatk4/splitncigarreads/main.nf b/tests/modules/nf-core/gatk4/splitncigarreads/main.nf index 31e45cec195..64e62a49d08 100644 --- a/tests/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/tests/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarreads/main.nf' +include { GATK4_SPLITNCIGARREADS } from '../../../../modules/nf-core/gatk4/splitncigarreads/main.nf' workflow test_gatk4_splitncigarreads { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/variantfiltration/main.nf b/tests/modules/nf-core/gatk4/variantfiltration/main.nf index 221c469acd0..8ec45813d8c 100644 --- a/tests/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/tests/modules/nf-core/gatk4/variantfiltration/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf' +include { GATK4_VARIANTFILTRATION } from '../../../../modules/nf-core/gatk4/variantfiltration/main.nf' // Basic parameters with uncompressed VCF input workflow test_gatk4_variantfiltration_vcf_input { diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf index 6ece09ebb5a..a492ae2f9f7 100644 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf' -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' workflow test_gatk4_variantrecalibrator { diff --git a/tests/modules/nf-core/gecco/run/main.nf b/tests/modules/nf-core/gecco/run/main.nf index 42ff5f3d9da..01f320df609 100644 --- a/tests/modules/nf-core/gecco/run/main.nf +++ b/tests/modules/nf-core/gecco/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GECCO_RUN } from '../../../../modules/gecco/run/main.nf' +include { GECCO_RUN } from '../../../../modules/nf-core/gecco/run/main.nf' workflow test_gecco_run { diff --git a/tests/modules/nf-core/genescopefk/main.nf b/tests/modules/nf-core/genescopefk/main.nf index e61b6d89252..72f10e566e9 100644 --- a/tests/modules/nf-core/genescopefk/main.nf +++ b/tests/modules/nf-core/genescopefk/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../modules/fastk/fastk/main.nf' -include { FASTK_HISTEX } from '../../../modules/fastk/histex/main.nf' -include { GENESCOPEFK } from '../../../modules/genescopefk/main.nf' +include { FASTK_FASTK } from '../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_HISTEX } from '../../../modules/nf-core/fastk/histex/main.nf' +include { GENESCOPEFK } from '../../../modules/nf-core/genescopefk/main.nf' workflow test_genescopefk { diff --git a/tests/modules/nf-core/genmap/index/main.nf b/tests/modules/nf-core/genmap/index/main.nf index 061066400f3..db7f85b3407 100644 --- a/tests/modules/nf-core/genmap/index/main.nf +++ b/tests/modules/nf-core/genmap/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' +include { GENMAP_INDEX } from '../../../../modules/nf-core/genmap/index/main.nf' workflow test_genmap_index { diff --git a/tests/modules/nf-core/genmap/mappability/main.nf b/tests/modules/nf-core/genmap/mappability/main.nf index eb6a34fadf0..aed4ed73bb9 100644 --- a/tests/modules/nf-core/genmap/mappability/main.nf +++ b/tests/modules/nf-core/genmap/mappability/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' -include { GENMAP_MAPPABILITY } from '../../../../modules/genmap/mappability/main.nf' +include { GENMAP_INDEX } from '../../../../modules/nf-core/genmap/index/main.nf' +include { GENMAP_MAPPABILITY } from '../../../../modules/nf-core/genmap/mappability/main.nf' workflow test_genmap_map { diff --git a/tests/modules/nf-core/genmod/annotate/main.nf b/tests/modules/nf-core/genmod/annotate/main.nf index 9e10c6b6995..d2a6190ae92 100644 --- a/tests/modules/nf-core/genmod/annotate/main.nf +++ b/tests/modules/nf-core/genmod/annotate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_ANNOTATE } from '../../../../modules/genmod/annotate/main.nf' +include { GENMOD_ANNOTATE } from '../../../../modules/nf-core/genmod/annotate/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genmod/compound/main.nf b/tests/modules/nf-core/genmod/compound/main.nf index 01ddbe7b6d1..fa817d412a2 100644 --- a/tests/modules/nf-core/genmod/compound/main.nf +++ b/tests/modules/nf-core/genmod/compound/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_COMPOUND } from '../../../../modules/genmod/compound/main.nf' +include { GENMOD_COMPOUND } from '../../../../modules/nf-core/genmod/compound/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genmod/models/main.nf b/tests/modules/nf-core/genmod/models/main.nf index 2566192e771..a7434557615 100644 --- a/tests/modules/nf-core/genmod/models/main.nf +++ b/tests/modules/nf-core/genmod/models/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_MODELS } from '../../../../modules/genmod/models/main.nf' +include { GENMOD_MODELS } from '../../../../modules/nf-core/genmod/models/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genmod/score/main.nf b/tests/modules/nf-core/genmod/score/main.nf index 798569e1536..5929ff475c7 100644 --- a/tests/modules/nf-core/genmod/score/main.nf +++ b/tests/modules/nf-core/genmod/score/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_SCORE } from '../../../../modules/genmod/score/main.nf' +include { GENMOD_SCORE } from '../../../../modules/nf-core/genmod/score/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genomescope2/main.nf b/tests/modules/nf-core/genomescope2/main.nf index 5ceebfd6bd3..b56b798fe91 100644 --- a/tests/modules/nf-core/genomescope2/main.nf +++ b/tests/modules/nf-core/genomescope2/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../modules/meryl/count/main.nf' -include { MERYL_HISTOGRAM } from '../../../modules/meryl/histogram/main.nf' -include { GENOMESCOPE2 } from '../../../modules/genomescope2/main.nf' +include { MERYL_COUNT } from '../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_HISTOGRAM } from '../../../modules/nf-core/meryl/histogram/main.nf' +include { GENOMESCOPE2 } from '../../../modules/nf-core/genomescope2/main.nf' workflow test_genomescope2 { diff --git a/tests/modules/nf-core/genotyphi/parse/main.nf b/tests/modules/nf-core/genotyphi/parse/main.nf index 761d18c1029..9eca9afee50 100644 --- a/tests/modules/nf-core/genotyphi/parse/main.nf +++ b/tests/modules/nf-core/genotyphi/parse/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf' -include { GENOTYPHI_PARSE } from '../../../../modules/genotyphi/parse/main.nf' +include { MYKROBE_PREDICT } from '../../../../modules/nf-core/mykrobe/predict/main.nf' +include { GENOTYPHI_PARSE } from '../../../../modules/nf-core/genotyphi/parse/main.nf' workflow test_mykrobe_predict { diff --git a/tests/modules/nf-core/genrich/main.nf b/tests/modules/nf-core/genrich/main.nf index 34db589e691..e7f9d5829ea 100644 --- a/tests/modules/nf-core/genrich/main.nf +++ b/tests/modules/nf-core/genrich/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GENRICH } from '../../../modules/genrich/main.nf' -include { GENRICH as GENRICH_CTRL } from '../../../modules/genrich/main.nf' -include { GENRICH as GENRICH_ALL } from '../../../modules/genrich/main.nf' -include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' +include { GENRICH } from '../../../modules/nf-core/genrich/main.nf' +include { GENRICH as GENRICH_CTRL } from '../../../modules/nf-core/genrich/main.nf' +include { GENRICH as GENRICH_ALL } from '../../../modules/nf-core/genrich/main.nf' +include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/nf-core/genrich/main.nf' workflow test_genrich { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/gfaffix/main.nf b/tests/modules/nf-core/gfaffix/main.nf index 333866c0bf0..43b833a418c 100644 --- a/tests/modules/nf-core/gfaffix/main.nf +++ b/tests/modules/nf-core/gfaffix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GFAFFIX } from '../../../modules/gfaffix/main.nf' +include { GFAFFIX } from '../../../modules/nf-core/gfaffix/main.nf' workflow test_gfaffix { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gffread/main.nf b/tests/modules/nf-core/gffread/main.nf index 6ab7922bcc2..5a3f2185765 100644 --- a/tests/modules/nf-core/gffread/main.nf +++ b/tests/modules/nf-core/gffread/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GFFREAD } from '../../../modules/gffread/main.nf' +include { GFFREAD } from '../../../modules/nf-core/gffread/main.nf' workflow test_gffread { input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) diff --git a/tests/modules/nf-core/glimpse/chunk/main.nf b/tests/modules/nf-core/glimpse/chunk/main.nf index 9edb2783d5d..c716ff35f67 100644 --- a/tests/modules/nf-core/glimpse/chunk/main.nf +++ b/tests/modules/nf-core/glimpse/chunk/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GLIMPSE_CHUNK } from '../../../../modules/glimpse/chunk/main.nf' +include { GLIMPSE_CHUNK } from '../../../../modules/nf-core/glimpse/chunk/main.nf' workflow test_glimpse_chunk { input = [ diff --git a/tests/modules/nf-core/glnexus/main.nf b/tests/modules/nf-core/glnexus/main.nf index aeb7c7e2e25..a85d8b37926 100644 --- a/tests/modules/nf-core/glnexus/main.nf +++ b/tests/modules/nf-core/glnexus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GLNEXUS } from '../../../modules/glnexus/main.nf' +include { GLNEXUS } from '../../../modules/nf-core/glnexus/main.nf' workflow test_glnexus { input = [ diff --git a/tests/modules/nf-core/goat/taxonsearch/main.nf b/tests/modules/nf-core/goat/taxonsearch/main.nf index 48f76f207ff..a58c9b24e55 100644 --- a/tests/modules/nf-core/goat/taxonsearch/main.nf +++ b/tests/modules/nf-core/goat/taxonsearch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GOAT_TAXONSEARCH } from '../../../../modules/goat/taxonsearch/main.nf' +include { GOAT_TAXONSEARCH } from '../../../../modules/nf-core/goat/taxonsearch/main.nf' // // Test with genus name (Canis) diff --git a/tests/modules/nf-core/graphmap2/align/main.nf b/tests/modules/nf-core/graphmap2/align/main.nf index 96b951660f0..fa44b8b2eae 100644 --- a/tests/modules/nf-core/graphmap2/align/main.nf +++ b/tests/modules/nf-core/graphmap2/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf' -include { GRAPHMAP2_ALIGN } from '../../../../modules/graphmap2/align/main.nf' +include { GRAPHMAP2_INDEX } from '../../../../modules/nf-core/graphmap2/index/main.nf' +include { GRAPHMAP2_ALIGN } from '../../../../modules/nf-core/graphmap2/align/main.nf' workflow test_graphmap2_align { diff --git a/tests/modules/nf-core/graphmap2/index/main.nf b/tests/modules/nf-core/graphmap2/index/main.nf index 3c449c6b853..b382ec4d96d 100644 --- a/tests/modules/nf-core/graphmap2/index/main.nf +++ b/tests/modules/nf-core/graphmap2/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf' +include { GRAPHMAP2_INDEX } from '../../../../modules/nf-core/graphmap2/index/main.nf' workflow test_graphmap2_index { diff --git a/tests/modules/nf-core/gstama/collapse/main.nf b/tests/modules/nf-core/gstama/collapse/main.nf index 3eb97767854..054518729d0 100644 --- a/tests/modules/nf-core/gstama/collapse/main.nf +++ b/tests/modules/nf-core/gstama/collapse/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GSTAMA_COLLAPSE } from '../../../../modules/gstama/collapse/main.nf' +include { GSTAMA_COLLAPSE } from '../../../../modules/nf-core/gstama/collapse/main.nf' workflow test_gstama_collapse { diff --git a/tests/modules/nf-core/gstama/merge/main.nf b/tests/modules/nf-core/gstama/merge/main.nf index 4a9102a29da..a892e23e3aa 100644 --- a/tests/modules/nf-core/gstama/merge/main.nf +++ b/tests/modules/nf-core/gstama/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GSTAMA_MERGE } from '../../../../modules/gstama/merge/main' +include { GSTAMA_MERGE } from '../../../../modules/nf-core/gstama/merge/main' workflow test_gstama_merge { diff --git a/tests/modules/nf-core/gstama/polyacleanup/main.nf b/tests/modules/nf-core/gstama/polyacleanup/main.nf index 67b3fa876ac..de05947db94 100644 --- a/tests/modules/nf-core/gstama/polyacleanup/main.nf +++ b/tests/modules/nf-core/gstama/polyacleanup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GSTAMA_POLYACLEANUP } from '../../../../modules/gstama/polyacleanup/main.nf' +include { GSTAMA_POLYACLEANUP } from '../../../../modules/nf-core/gstama/polyacleanup/main.nf' workflow test_gstama_polyacleanup { diff --git a/tests/modules/nf-core/gtdbtk/classifywf/main.nf b/tests/modules/nf-core/gtdbtk/classifywf/main.nf index 1517d7cc9a4..f84a8b2f789 100644 --- a/tests/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/tests/modules/nf-core/gtdbtk/classifywf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GTDBTK_CLASSIFYWF } from '../../../../modules/gtdbtk/classifywf/main.nf' +include { GTDBTK_CLASSIFYWF } from '../../../../modules/nf-core/gtdbtk/classifywf/main.nf' process STUB_GTDBTK_DATABASE { output: diff --git a/tests/modules/nf-core/gubbins/main.nf b/tests/modules/nf-core/gubbins/main.nf index 342150b383f..74993ac943e 100644 --- a/tests/modules/nf-core/gubbins/main.nf +++ b/tests/modules/nf-core/gubbins/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GUBBINS } from '../../../modules/gubbins/main.nf' +include { GUBBINS } from '../../../modules/nf-core/gubbins/main.nf' workflow test_gubbins { input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true) diff --git a/tests/modules/nf-core/gunc/downloaddb/main.nf b/tests/modules/nf-core/gunc/downloaddb/main.nf index 3e3126f538d..0861a9111bc 100644 --- a/tests/modules/nf-core/gunc/downloaddb/main.nf +++ b/tests/modules/nf-core/gunc/downloaddb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf' +include { GUNC_DOWNLOADDB } from '../../../../modules/nf-core/gunc/downloaddb/main.nf' workflow test_gunc_downloaddb { diff --git a/tests/modules/nf-core/gunc/run/main.nf b/tests/modules/nf-core/gunc/run/main.nf index 28ecd35fea6..f7a10825fc2 100644 --- a/tests/modules/nf-core/gunc/run/main.nf +++ b/tests/modules/nf-core/gunc/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GUNC_RUN } from '../../../../modules/gunc/run/main.nf' -include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf' +include { GUNC_RUN } from '../../../../modules/nf-core/gunc/run/main.nf' +include { GUNC_DOWNLOADDB } from '../../../../modules/nf-core/gunc/downloaddb/main.nf' workflow test_gunc_run { diff --git a/tests/modules/nf-core/gunzip/main.nf b/tests/modules/nf-core/gunzip/main.nf index 3d41a4a2055..1a1af3b5ca2 100644 --- a/tests/modules/nf-core/gunzip/main.nf +++ b/tests/modules/nf-core/gunzip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/gunzip/main.nf' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' workflow test_gunzip { input = [ [], diff --git a/tests/modules/nf-core/gvcftools/extractvariants/main.nf b/tests/modules/nf-core/gvcftools/extractvariants/main.nf index b614072f5b3..acad43faf16 100644 --- a/tests/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/tests/modules/nf-core/gvcftools/extractvariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GVCFTOOLS_EXTRACTVARIANTS } from '../../../../modules/gvcftools/extractvariants/main.nf' +include { GVCFTOOLS_EXTRACTVARIANTS } from '../../../../modules/nf-core/gvcftools/extractvariants/main.nf' workflow test_gvcftools_extractvariants { diff --git a/tests/modules/nf-core/hamronization/abricate/main.nf b/tests/modules/nf-core/hamronization/abricate/main.nf index 111824697e1..aeb667de1b1 100644 --- a/tests/modules/nf-core/hamronization/abricate/main.nf +++ b/tests/modules/nf-core/hamronization/abricate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAMRONIZATION_ABRICATE } from '../../../../modules/hamronization/abricate/main.nf' +include { HAMRONIZATION_ABRICATE } from '../../../../modules/nf-core/hamronization/abricate/main.nf' workflow test_hamronization_abricate { diff --git a/tests/modules/nf-core/hamronization/amrfinderplus/main.nf b/tests/modules/nf-core/hamronization/amrfinderplus/main.nf index cb477847457..e63cc558173 100644 --- a/tests/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/tests/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../modules/hamronization/amrfinderplus/main.nf' +include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../modules/nf-core/hamronization/amrfinderplus/main.nf' workflow test_hamronization_amrfinderplus { diff --git a/tests/modules/nf-core/hamronization/deeparg/main.nf b/tests/modules/nf-core/hamronization/deeparg/main.nf index 3f674bbc0c9..6f4f196069e 100644 --- a/tests/modules/nf-core/hamronization/deeparg/main.nf +++ b/tests/modules/nf-core/hamronization/deeparg/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf' +include { HAMRONIZATION_DEEPARG } from '../../../../modules/nf-core/hamronization/deeparg/main.nf' workflow test_hamronization_deeparg { diff --git a/tests/modules/nf-core/hamronization/fargene/main.nf b/tests/modules/nf-core/hamronization/fargene/main.nf index f54a4534c30..599585ea2f9 100644 --- a/tests/modules/nf-core/hamronization/fargene/main.nf +++ b/tests/modules/nf-core/hamronization/fargene/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/gunzip/main.nf' -include { FARGENE } from '../../../modules/fargene/main.nf' -include { HAMRONIZATION_FARGENE } from '../../../../modules/hamronization/fargene/main.nf' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' +include { FARGENE } from '../../../modules/nf-core/fargene/main.nf' +include { HAMRONIZATION_FARGENE } from '../../../../modules/nf-core/hamronization/fargene/main.nf' workflow test_hamronization_fargene { diff --git a/tests/modules/nf-core/hamronization/rgi/main.nf b/tests/modules/nf-core/hamronization/rgi/main.nf index 1940e4a3f47..4407d0f9cd2 100644 --- a/tests/modules/nf-core/hamronization/rgi/main.nf +++ b/tests/modules/nf-core/hamronization/rgi/main.nf @@ -1,8 +1,8 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf' -include { HAMRONIZATION_RGI } from '../../../../modules/hamronization/rgi/main.nf' +include { RGI_MAIN } from '../../../../modules/nf-core/rgi/main/main.nf' +include { HAMRONIZATION_RGI } from '../../../../modules/nf-core/hamronization/rgi/main.nf' workflow test_hamronization_rgi { diff --git a/tests/modules/nf-core/hamronization/summarize/main.nf b/tests/modules/nf-core/hamronization/summarize/main.nf index aeb46991bbf..67f57675352 100644 --- a/tests/modules/nf-core/hamronization/summarize/main.nf +++ b/tests/modules/nf-core/hamronization/summarize/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf' -include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/hamronization/deeparg/main.nf' -include { HAMRONIZATION_SUMMARIZE } from '../../../../modules/hamronization/summarize/main.nf' +include { HAMRONIZATION_DEEPARG } from '../../../../modules/nf-core/hamronization/deeparg/main.nf' +include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/nf-core/hamronization/deeparg/main.nf' +include { HAMRONIZATION_SUMMARIZE } from '../../../../modules/nf-core/hamronization/summarize/main.nf' workflow test_hamronization_summarize { diff --git a/tests/modules/nf-core/haplocheck/main.nf b/tests/modules/nf-core/haplocheck/main.nf index 9699c33c516..cde2586ba14 100644 --- a/tests/modules/nf-core/haplocheck/main.nf +++ b/tests/modules/nf-core/haplocheck/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPLOCHECK } from '../../../modules/haplocheck/main.nf' +include { HAPLOCHECK } from '../../../modules/nf-core/haplocheck/main.nf' workflow test_haplocheck { diff --git a/tests/modules/nf-core/haplogrep2/classify/main.nf b/tests/modules/nf-core/haplogrep2/classify/main.nf index 89f45f36127..ebb844863fb 100644 --- a/tests/modules/nf-core/haplogrep2/classify/main.nf +++ b/tests/modules/nf-core/haplogrep2/classify/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPLOGREP2_CLASSIFY } from '../../../../modules/haplogrep2/classify/main.nf' +include { HAPLOGREP2_CLASSIFY } from '../../../../modules/nf-core/haplogrep2/classify/main.nf' workflow test_haplogrep2_classify { diff --git a/tests/modules/nf-core/happy/happy/main.nf b/tests/modules/nf-core/happy/happy/main.nf index 515a657bb5c..e31511197ed 100644 --- a/tests/modules/nf-core/happy/happy/main.nf +++ b/tests/modules/nf-core/happy/happy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPPY_HAPPY } from '../../../../modules/happy/happy/main.nf' +include { HAPPY_HAPPY } from '../../../../modules/nf-core/happy/happy/main.nf' workflow test_happy_vcf { diff --git a/tests/modules/nf-core/happy/prepy/main.nf b/tests/modules/nf-core/happy/prepy/main.nf index 0b511104e9d..d3f9b63f123 100644 --- a/tests/modules/nf-core/happy/prepy/main.nf +++ b/tests/modules/nf-core/happy/prepy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPPY_PREPY } from '../../../../modules/happy/prepy/main.nf' +include { HAPPY_PREPY } from '../../../../modules/nf-core/happy/prepy/main.nf' workflow test_happy_prepy_vcf { diff --git a/tests/modules/nf-core/hicap/main.nf b/tests/modules/nf-core/hicap/main.nf index 82c515de49b..46e797534f3 100644 --- a/tests/modules/nf-core/hicap/main.nf +++ b/tests/modules/nf-core/hicap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HICAP } from '../../../modules/hicap/main.nf' +include { HICAP } from '../../../modules/nf-core/hicap/main.nf' workflow test_hicap { diff --git a/tests/modules/nf-core/hifiasm/main.nf b/tests/modules/nf-core/hifiasm/main.nf index f0e2a0f4499..1d4cb18e0f5 100644 --- a/tests/modules/nf-core/hifiasm/main.nf +++ b/tests/modules/nf-core/hifiasm/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HIFIASM } from '../../../modules/hifiasm/main.nf' +include { HIFIASM } from '../../../modules/nf-core/hifiasm/main.nf' /* * Test with long reads only diff --git a/tests/modules/nf-core/hisat2/align/main.nf b/tests/modules/nf-core/hisat2/align/main.nf index 17b47c93606..df406883400 100644 --- a/tests/modules/nf-core/hisat2/align/main.nf +++ b/tests/modules/nf-core/hisat2/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' -include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf' -include { HISAT2_ALIGN } from '../../../../modules/hisat2/align/main.nf' +include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' +include { HISAT2_BUILD } from '../../../../modules/nf-core/hisat2/build/main.nf' +include { HISAT2_ALIGN } from '../../../../modules/nf-core/hisat2/align/main.nf' workflow test_hisat2_align_single_end { input = [ diff --git a/tests/modules/nf-core/hisat2/build_test/main.nf b/tests/modules/nf-core/hisat2/build_test/main.nf index a0c14dc863d..f43bd8c6014 100644 --- a/tests/modules/nf-core/hisat2/build_test/main.nf +++ b/tests/modules/nf-core/hisat2/build_test/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' -include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf' +include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' +include { HISAT2_BUILD } from '../../../../modules/nf-core/hisat2/build/main.nf' workflow test_hisat2_build { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/hisat2/extractsplicesites/main.nf b/tests/modules/nf-core/hisat2/extractsplicesites/main.nf index e947717ee4a..a7203de85bc 100644 --- a/tests/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/tests/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' +include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' workflow test_hisat2_extractsplicesites { gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) diff --git a/tests/modules/nf-core/hmmcopy/gccounter/main.nf b/tests/modules/nf-core/hmmcopy/gccounter/main.nf index 05728bf52f0..0b635a9b764 100644 --- a/tests/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/tests/modules/nf-core/hmmcopy/gccounter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf' +include { HMMCOPY_GCCOUNTER } from '../../../../modules/nf-core/hmmcopy/gccounter/main.nf' workflow test_hmmcopy_gccounter { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/hmmcopy/generatemap/main.nf b/tests/modules/nf-core/hmmcopy/generatemap/main.nf index 381420d35bd..122b6b21722 100644 --- a/tests/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/tests/modules/nf-core/hmmcopy/generatemap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../modules/nf-core/hmmcopy/generatemap/main.nf' workflow test_hmmcopy_generatemap { diff --git a/tests/modules/nf-core/hmmcopy/mapcounter/main.nf b/tests/modules/nf-core/hmmcopy/mapcounter/main.nf index c364f0f7234..11a8dffb64e 100644 --- a/tests/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/tests/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf' -include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf' +include { HMMCOPY_MAPCOUNTER } from '../../../../modules/nf-core/hmmcopy/mapcounter/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../modules/nf-core/hmmcopy/generatemap/main.nf' workflow test_hmmcopy_mapcounter { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/hmmcopy/readcounter/main.nf b/tests/modules/nf-core/hmmcopy/readcounter/main.nf index 21737aabaed..7aa28ace0a9 100644 --- a/tests/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/tests/modules/nf-core/hmmcopy/readcounter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf' +include { HMMCOPY_READCOUNTER } from '../../../../modules/nf-core/hmmcopy/readcounter/main.nf' workflow test_hmmcopy_readcounter { diff --git a/tests/modules/nf-core/hmmer/eslalimask/main.nf b/tests/modules/nf-core/hmmer/eslalimask/main.nf index 6a37b345028..c84ba730b26 100644 --- a/tests/modules/nf-core/hmmer/eslalimask/main.nf +++ b/tests/modules/nf-core/hmmer/eslalimask/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMALIGN } from '../../../../modules/hmmer/hmmalign/main.nf' -include { HMMER_ESLALIMASK as RFMASK } from '../../../../modules/hmmer/eslalimask/main.nf' +include { HMMER_HMMALIGN } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_ESLALIMASK as RFMASK } from '../../../../modules/nf-core/hmmer/eslalimask/main.nf' workflow test_hmmer_rfmask { diff --git a/tests/modules/nf-core/hmmer/eslreformat/main.nf b/tests/modules/nf-core/hmmer/eslreformat/main.nf index aa1d3d690f3..a70c318227f 100644 --- a/tests/modules/nf-core/hmmer/eslreformat/main.nf +++ b/tests/modules/nf-core/hmmer/eslreformat/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMALIGN } from '../../../../modules/hmmer/hmmalign/main.nf' -include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_AFA } from '../../../../modules/hmmer/eslreformat/main.nf' -include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_PHYLIP } from '../../../../modules/hmmer/eslreformat/main.nf' -include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_UNALIGN } from '../../../../modules/hmmer/eslreformat/main.nf' +include { HMMER_HMMALIGN } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_AFA } from '../../../../modules/nf-core/hmmer/eslreformat/main.nf' +include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_PHYLIP } from '../../../../modules/nf-core/hmmer/eslreformat/main.nf' +include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_UNALIGN } from '../../../../modules/nf-core/hmmer/eslreformat/main.nf' workflow test_hmmer_eslreformat_afa { diff --git a/tests/modules/nf-core/hmmer/hmmalign/main.nf b/tests/modules/nf-core/hmmer/hmmalign/main.nf index 7e48d00a338..08d8717750b 100644 --- a/tests/modules/nf-core/hmmer/hmmalign/main.nf +++ b/tests/modules/nf-core/hmmer/hmmalign/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMALIGN as HMMER_HMMALIGN } from '../../../../modules/hmmer/hmmalign/main.nf' -include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../modules/hmmer/hmmalign/main.nf' +include { HMMER_HMMALIGN as HMMER_HMMALIGN } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' workflow test_hmmer_hmmalign { diff --git a/tests/modules/nf-core/hmmer/hmmbuild/main.nf b/tests/modules/nf-core/hmmer/hmmbuild/main.nf index 15fb04c6af9..dc4b0e8e6ab 100644 --- a/tests/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/tests/modules/nf-core/hmmer/hmmbuild/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMBUILD } from '../../../../modules/hmmer/hmmbuild/main.nf' +include { HMMER_HMMBUILD } from '../../../../modules/nf-core/hmmer/hmmbuild/main.nf' workflow test_hmmer_hmmbuild { diff --git a/tests/modules/nf-core/hmmer/hmmsearch/main.nf b/tests/modules/nf-core/hmmer/hmmsearch/main.nf index b181a529ca3..518031ce7e8 100644 --- a/tests/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/tests/modules/nf-core/hmmer/hmmsearch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMSEARCH } from '../../../../modules/hmmer/hmmsearch/main.nf' +include { HMMER_HMMSEARCH } from '../../../../modules/nf-core/hmmer/hmmsearch/main.nf' workflow test_hmmer_hmmsearch { diff --git a/tests/modules/nf-core/hmtnote/main.nf b/tests/modules/nf-core/hmtnote/main.nf index 9bee719c415..d914e6d02db 100644 --- a/tests/modules/nf-core/hmtnote/main.nf +++ b/tests/modules/nf-core/hmtnote/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMTNOTE } from '../../../modules/hmtnote/main.nf' +include { HMTNOTE } from '../../../modules/nf-core/hmtnote/main.nf' workflow test_hmtnote { diff --git a/tests/modules/nf-core/homer/annotatepeaks/main.nf b/tests/modules/nf-core/homer/annotatepeaks/main.nf index ab8f6f8f19a..5f0bdbdb744 100644 --- a/tests/modules/nf-core/homer/annotatepeaks/main.nf +++ b/tests/modules/nf-core/homer/annotatepeaks/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HOMER_ANNOTATEPEAKS } from '../../../../modules/homer/annotatepeaks/main.nf' +include { HOMER_ANNOTATEPEAKS } from '../../../../modules/nf-core/homer/annotatepeaks/main.nf' workflow test_homer_annotatepeaks { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/homer/findpeaks/main.nf b/tests/modules/nf-core/homer/findpeaks/main.nf index 0e7e8ed6d4f..b1db0814cbd 100644 --- a/tests/modules/nf-core/homer/findpeaks/main.nf +++ b/tests/modules/nf-core/homer/findpeaks/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' -include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf' +include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' +include { HOMER_FINDPEAKS } from '../../../../modules/nf-core/homer/findpeaks/main.nf' workflow test_homer_findpeaks { input = [[id:'test'], diff --git a/tests/modules/nf-core/homer/maketagdirectory/main.nf b/tests/modules/nf-core/homer/maketagdirectory/main.nf index 7de693e6a1b..cf0950c2bf8 100644 --- a/tests/modules/nf-core/homer/maketagdirectory/main.nf +++ b/tests/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BED HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BAM -} from '../../../../modules/homer/maketagdirectory/main.nf' +} from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' workflow test_homer_maketagdirectory_bed { input = [[id:'test'], diff --git a/tests/modules/nf-core/homer/makeucscfile/main.nf b/tests/modules/nf-core/homer/makeucscfile/main.nf index 986c9c14d34..243687696b1 100644 --- a/tests/modules/nf-core/homer/makeucscfile/main.nf +++ b/tests/modules/nf-core/homer/makeucscfile/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' -include { HOMER_MAKEUCSCFILE } from '../../../../modules/homer/makeucscfile/main.nf' +include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' +include { HOMER_MAKEUCSCFILE } from '../../../../modules/nf-core/homer/makeucscfile/main.nf' workflow test_homer_makeucscfile { input = [[id:'test'], diff --git a/tests/modules/nf-core/homer/pos2bed/main.nf b/tests/modules/nf-core/homer/pos2bed/main.nf index bcfdc0bc0fa..3d814f60728 100644 --- a/tests/modules/nf-core/homer/pos2bed/main.nf +++ b/tests/modules/nf-core/homer/pos2bed/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' -include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf' -include { HOMER_POS2BED } from '../../../../modules/homer/pos2bed/main.nf' +include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' +include { HOMER_FINDPEAKS } from '../../../../modules/nf-core/homer/findpeaks/main.nf' +include { HOMER_POS2BED } from '../../../../modules/nf-core/homer/pos2bed/main.nf' workflow test_homer_pos2bed { input = [[id:'test'], diff --git a/tests/modules/nf-core/hpsuissero/main.nf b/tests/modules/nf-core/hpsuissero/main.nf index f66fcd9368e..03cde9e7bfe 100644 --- a/tests/modules/nf-core/hpsuissero/main.nf +++ b/tests/modules/nf-core/hpsuissero/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf' +include { HPSUISSERO } from '../../../modules/nf-core/hpsuissero/main.nf' workflow test_hpsuissero { diff --git a/tests/modules/nf-core/ichorcna/createpon/main.nf b/tests/modules/nf-core/ichorcna/createpon/main.nf index 0e86fb92c4a..b5fadf62ecb 100644 --- a/tests/modules/nf-core/ichorcna/createpon/main.nf +++ b/tests/modules/nf-core/ichorcna/createpon/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ICHORCNA_CREATEPON } from '../../../../modules/ichorcna/createpon/main.nf' +include { ICHORCNA_CREATEPON } from '../../../../modules/nf-core/ichorcna/createpon/main.nf' workflow test_ichorcna_createpon { diff --git a/tests/modules/nf-core/ichorcna/run/main.nf b/tests/modules/nf-core/ichorcna/run/main.nf index 8a830f62451..fc87f133b9d 100644 --- a/tests/modules/nf-core/ichorcna/run/main.nf +++ b/tests/modules/nf-core/ichorcna/run/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { ICHORCNA_RUN } from '../../../../modules/ichorcna/run/main.nf' -include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf' -include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf' -include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf' -include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf' +include { ICHORCNA_RUN } from '../../../../modules/nf-core/ichorcna/run/main.nf' +include { HMMCOPY_READCOUNTER } from '../../../../modules/nf-core/hmmcopy/readcounter/main.nf' +include { HMMCOPY_GCCOUNTER } from '../../../../modules/nf-core/hmmcopy/gccounter/main.nf' +include { HMMCOPY_MAPCOUNTER } from '../../../../modules/nf-core/hmmcopy/mapcounter/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../modules/nf-core/hmmcopy/generatemap/main.nf' workflow test_ichorcna_run_no_panel { diff --git a/tests/modules/nf-core/idr/main.nf b/tests/modules/nf-core/idr/main.nf index ed3bf289ead..67998a1a641 100644 --- a/tests/modules/nf-core/idr/main.nf +++ b/tests/modules/nf-core/idr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IDR } from '../../../modules/idr/main.nf' +include { IDR } from '../../../modules/nf-core/idr/main.nf' workflow test_idr_narrowpeak { diff --git a/tests/modules/nf-core/imputeme/vcftoprs/main.nf b/tests/modules/nf-core/imputeme/vcftoprs/main.nf index dccc06e0e25..a42061bbe6a 100644 --- a/tests/modules/nf-core/imputeme/vcftoprs/main.nf +++ b/tests/modules/nf-core/imputeme/vcftoprs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IMPUTEME_VCFTOPRS } from '../../../../modules/imputeme/vcftoprs/main.nf' +include { IMPUTEME_VCFTOPRS } from '../../../../modules/nf-core/imputeme/vcftoprs/main.nf' workflow test_imputeme_vcftoprs { diff --git a/tests/modules/nf-core/instrain/profile/main.nf b/tests/modules/nf-core/instrain/profile/main.nf index ce054725efa..f5f4aba4350 100644 --- a/tests/modules/nf-core/instrain/profile/main.nf +++ b/tests/modules/nf-core/instrain/profile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { INSTRAIN_PROFILE } from '../../../../modules/instrain/profile/main.nf' +include { INSTRAIN_PROFILE } from '../../../../modules/nf-core/instrain/profile/main.nf' workflow test_instrain_profile { diff --git a/tests/modules/nf-core/iqtree/main.nf b/tests/modules/nf-core/iqtree/main.nf index 2d73bd52c77..071965b8cb1 100644 --- a/tests/modules/nf-core/iqtree/main.nf +++ b/tests/modules/nf-core/iqtree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IQTREE } from '../../../modules/iqtree/main.nf' +include { IQTREE } from '../../../modules/nf-core/iqtree/main.nf' workflow test_iqtree { diff --git a/tests/modules/nf-core/ismapper/main.nf b/tests/modules/nf-core/ismapper/main.nf index abb180f746c..5f816e18c80 100644 --- a/tests/modules/nf-core/ismapper/main.nf +++ b/tests/modules/nf-core/ismapper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ISMAPPER } from '../../../modules/ismapper/main.nf' +include { ISMAPPER } from '../../../modules/nf-core/ismapper/main.nf' workflow test_ismapper { diff --git a/tests/modules/nf-core/isoseq3/cluster/main.nf b/tests/modules/nf-core/isoseq3/cluster/main.nf index 958b03a6b2c..82cce6665e5 100644 --- a/tests/modules/nf-core/isoseq3/cluster/main.nf +++ b/tests/modules/nf-core/isoseq3/cluster/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ISOSEQ3_CLUSTER } from '../../../../modules/isoseq3/cluster/main.nf' +include { ISOSEQ3_CLUSTER } from '../../../../modules/nf-core/isoseq3/cluster/main.nf' workflow test_isoseq3_cluster { diff --git a/tests/modules/nf-core/isoseq3/refine/main.nf b/tests/modules/nf-core/isoseq3/refine/main.nf index 45dd1560f11..da96361e67f 100644 --- a/tests/modules/nf-core/isoseq3/refine/main.nf +++ b/tests/modules/nf-core/isoseq3/refine/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ISOSEQ3_REFINE } from '../../../../modules/isoseq3/refine/main' +include { ISOSEQ3_REFINE } from '../../../../modules/nf-core/isoseq3/refine/main' workflow test_isoseq3_refine { diff --git a/tests/modules/nf-core/ivar/consensus/main.nf b/tests/modules/nf-core/ivar/consensus/main.nf index 27ac83f9917..ec75d8c3f36 100644 --- a/tests/modules/nf-core/ivar/consensus/main.nf +++ b/tests/modules/nf-core/ivar/consensus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf' +include { IVAR_CONSENSUS } from '../../../../modules/nf-core/ivar/consensus/main.nf' workflow test_ivar_consensus { diff --git a/tests/modules/nf-core/ivar/trim/main.nf b/tests/modules/nf-core/ivar/trim/main.nf index 15d0e73956d..915cf904ee7 100644 --- a/tests/modules/nf-core/ivar/trim/main.nf +++ b/tests/modules/nf-core/ivar/trim/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IVAR_TRIM } from '../../../../modules/ivar/trim/main.nf' +include { IVAR_TRIM } from '../../../../modules/nf-core/ivar/trim/main.nf' workflow test_ivar_trim { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/ivar/variants/main.nf b/tests/modules/nf-core/ivar/variants/main.nf index 2d8e77c5dca..bd3c4f05019 100644 --- a/tests/modules/nf-core/ivar/variants/main.nf +++ b/tests/modules/nf-core/ivar/variants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf' +include { IVAR_VARIANTS } from '../../../../modules/nf-core/ivar/variants/main.nf' workflow test_ivar_variants_no_gff_no_mpileup { diff --git a/tests/modules/nf-core/jupyternotebook/main.nf b/tests/modules/nf-core/jupyternotebook/main.nf index 1db9d812f0e..c5fe8a3988c 100644 --- a/tests/modules/nf-core/jupyternotebook/main.nf +++ b/tests/modules/nf-core/jupyternotebook/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { JUPYTERNOTEBOOK } from '../../../modules/jupyternotebook/main.nf' -include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/jupyternotebook/main.nf' -include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/jupyternotebook/main.nf' +include { JUPYTERNOTEBOOK } from '../../../modules/nf-core/jupyternotebook/main.nf' +include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/nf-core/jupyternotebook/main.nf' +include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/nf-core/jupyternotebook/main.nf' workflow test_jupyternotebook { diff --git a/tests/modules/nf-core/kaiju/kaiju/main.nf b/tests/modules/nf-core/kaiju/kaiju/main.nf index 10849ff8ab9..48b8e7e13fc 100644 --- a/tests/modules/nf-core/kaiju/kaiju/main.nf +++ b/tests/modules/nf-core/kaiju/kaiju/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { KAIJU_KAIJU } from '../../../../modules/nf-core/kaiju/kaiju/main.nf' workflow test_kaiju_kaiju_single_end { diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf index aabefd1fc33..a56e8d193a6 100644 --- a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf' -include { KAIJU_KAIJU2KRONA } from '../../../../modules/kaiju/kaiju2krona/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { KAIJU_KAIJU } from '../../../../modules/nf-core/kaiju/kaiju/main.nf' +include { KAIJU_KAIJU2KRONA } from '../../../../modules/nf-core/kaiju/kaiju2krona/main.nf' workflow test_kaiju_kaiju2krona { diff --git a/tests/modules/nf-core/kaiju/kaiju2table/main.nf b/tests/modules/nf-core/kaiju/kaiju2table/main.nf index b7169ba51ec..b8d51be81ac 100644 --- a/tests/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/tests/modules/nf-core/kaiju/kaiju2table/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf' -include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { KAIJU_KAIJU } from '../../../../modules/nf-core/kaiju/kaiju/main.nf' +include { KAIJU_KAIJU2TABLE } from '../../../../modules/nf-core/kaiju/kaiju2table/main.nf' workflow test_kaiju_kaiju_single_end { diff --git a/tests/modules/nf-core/kallisto/index/main.nf b/tests/modules/nf-core/kallisto/index/main.nf index 8ecd6d526c6..83f51efcfed 100644 --- a/tests/modules/nf-core/kallisto/index/main.nf +++ b/tests/modules/nf-core/kallisto/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf' +include { KALLISTO_INDEX } from '../../../../modules/nf-core/kallisto/index/main.nf' workflow test_kallisto_index { diff --git a/tests/modules/nf-core/kallistobustools/count/main.nf b/tests/modules/nf-core/kallistobustools/count/main.nf index 1dd55cb3f6b..9f193b564c9 100644 --- a/tests/modules/nf-core/kallistobustools/count/main.nf +++ b/tests/modules/nf-core/kallistobustools/count/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { KALLISTOBUSTOOLS_REF } from '../../../../modules/kallistobustools/ref/main.nf' -include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' +include { KALLISTOBUSTOOLS_REF } from '../../../../modules/nf-core/kallistobustools/ref/main.nf' +include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/nf-core/kallistobustools/count/main.nf' workflow test_kallistobustools_count { diff --git a/tests/modules/nf-core/kallistobustools/ref/main.nf b/tests/modules/nf-core/kallistobustools/ref/main.nf index 09ea68ea8fa..0d6d1c69c19 100644 --- a/tests/modules/nf-core/kallistobustools/ref/main.nf +++ b/tests/modules/nf-core/kallistobustools/ref/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KALLISTOBUSTOOLS_REF } from '../../../../modules/kallistobustools/ref/main.nf' +include { KALLISTOBUSTOOLS_REF } from '../../../../modules/nf-core/kallistobustools/ref/main.nf' workflow test_kallistobustools_ref_standard { diff --git a/tests/modules/nf-core/kat/hist/main.nf b/tests/modules/nf-core/kat/hist/main.nf index 88136749ba8..9c1356700b6 100644 --- a/tests/modules/nf-core/kat/hist/main.nf +++ b/tests/modules/nf-core/kat/hist/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KAT_HIST } from '../../../../modules/kat/hist/main.nf' +include { KAT_HIST } from '../../../../modules/nf-core/kat/hist/main.nf' workflow test_kat_hist_single_end { diff --git a/tests/modules/nf-core/khmer/normalizebymedian/main.nf b/tests/modules/nf-core/khmer/normalizebymedian/main.nf index c439c40f6e3..c26fb09f0ba 100644 --- a/tests/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/tests/modules/nf-core/khmer/normalizebymedian/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf' -include { KHMER_NORMALIZEBYMEDIAN } from '../../../../modules/khmer/normalizebymedian/main.nf' -include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../modules/khmer/normalizebymedian/main.nf' +include { SEQTK_MERGEPE } from '../../../../modules/nf-core/seqtk/mergepe/main.nf' +include { KHMER_NORMALIZEBYMEDIAN } from '../../../../modules/nf-core/khmer/normalizebymedian/main.nf' +include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../modules/nf-core/khmer/normalizebymedian/main.nf' workflow test_khmer_normalizebymedian_only_pe { diff --git a/tests/modules/nf-core/khmer/uniquekmers/main.nf b/tests/modules/nf-core/khmer/uniquekmers/main.nf index cfd6de9f483..afcbe13bc60 100644 --- a/tests/modules/nf-core/khmer/uniquekmers/main.nf +++ b/tests/modules/nf-core/khmer/uniquekmers/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KHMER_UNIQUEKMERS } from '../../../../modules/khmer/uniquekmers/main.nf' +include { KHMER_UNIQUEKMERS } from '../../../../modules/nf-core/khmer/uniquekmers/main.nf' workflow test_khmer_uniquekmers { diff --git a/tests/modules/nf-core/kleborate/main.nf b/tests/modules/nf-core/kleborate/main.nf index bce31225908..c50153bdfc4 100644 --- a/tests/modules/nf-core/kleborate/main.nf +++ b/tests/modules/nf-core/kleborate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KLEBORATE } from '../../../modules/kleborate/main.nf' +include { KLEBORATE } from '../../../modules/nf-core/kleborate/main.nf' workflow test_kleborate { diff --git a/tests/modules/nf-core/kraken2/kraken2/main.nf b/tests/modules/nf-core/kraken2/kraken2/main.nf index 4a3593e40f6..4570817668c 100644 --- a/tests/modules/nf-core/kraken2/kraken2/main.nf +++ b/tests/modules/nf-core/kraken2/kraken2/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main.nf' workflow test_kraken2_kraken2_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/krakentools/combinekreports/main.nf b/tests/modules/nf-core/krakentools/combinekreports/main.nf index 6a1f829084d..6cb92667848 100644 --- a/tests/modules/nf-core/krakentools/combinekreports/main.nf +++ b/tests/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main' -include { KRAKENTOOLS_COMBINEKREPORTS } from '../../../../modules/krakentools/combinekreports/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main' +include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main' +include { KRAKENTOOLS_COMBINEKREPORTS } from '../../../../modules/nf-core/krakentools/combinekreports/main.nf' workflow test_krakentools_combinekreports { diff --git a/tests/modules/nf-core/krakentools/kreport2krona/main.nf b/tests/modules/nf-core/krakentools/kreport2krona/main.nf index c9c626fdf16..28f79ea08a2 100644 --- a/tests/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/tests/modules/nf-core/krakentools/kreport2krona/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main' -include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../modules/krakentools/kreport2krona/main' +include { UNTAR } from '../../../../modules/nf-core/untar/main' +include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main' +include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../modules/nf-core/krakentools/kreport2krona/main' workflow test_krakentools_kreport2krona { diff --git a/tests/modules/nf-core/krona/kronadb/main.nf b/tests/modules/nf-core/krona/kronadb/main.nf index ed95585400a..2a701b5cb6f 100644 --- a/tests/modules/nf-core/krona/kronadb/main.nf +++ b/tests/modules/nf-core/krona/kronadb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KRONA_KRONADB } from '../../../../modules/krona/kronadb/main.nf' +include { KRONA_KRONADB } from '../../../../modules/nf-core/krona/kronadb/main.nf' workflow test_krona_kronadb { KRONA_KRONADB ( ) diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf index 7b39ee821ff..e9029b6f802 100644 --- a/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS } from '../../../../modules/krona/ktimporttaxonomy/main.nf' -include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf' +include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS } from '../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf' +include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf' workflow test_krona_ktimporttaxonomy_reads { diff --git a/tests/modules/nf-core/krona/ktimporttext/main.nf b/tests/modules/nf-core/krona/ktimporttext/main.nf index 3d288b7b5d0..fef8403811c 100644 --- a/tests/modules/nf-core/krona/ktimporttext/main.nf +++ b/tests/modules/nf-core/krona/ktimporttext/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KRONA_KTIMPORTTEXT } from '../../../../modules/krona/ktimporttext/main.nf' +include { KRONA_KTIMPORTTEXT } from '../../../../modules/nf-core/krona/ktimporttext/main.nf' workflow test_krona_ktimporttext_multi { diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf index d2d18f3145c..b1165675f3f 100644 --- a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/krona/ktupdatetaxonomy/main.nf' +include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/nf-core/krona/ktupdatetaxonomy/main.nf' workflow test_krona_ktupdatetaxonomy { KRONA_KTUPDATETAXONOMY ( ) diff --git a/tests/modules/nf-core/last/dotplot/main.nf b/tests/modules/nf-core/last/dotplot/main.nf index 3353821d76b..ced2e579994 100644 --- a/tests/modules/nf-core/last/dotplot/main.nf +++ b/tests/modules/nf-core/last/dotplot/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_DOTPLOT } from '../../../../modules/last/dotplot/main.nf' +include { LAST_DOTPLOT } from '../../../../modules/nf-core/last/dotplot/main.nf' workflow test_last_dotplot { diff --git a/tests/modules/nf-core/last/lastal/main.nf b/tests/modules/nf-core/last/lastal/main.nf index 76e124c38f6..b47518f3b5c 100644 --- a/tests/modules/nf-core/last/lastal/main.nf +++ b/tests/modules/nf-core/last/lastal/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { LAST_LASTAL } from '../../../../modules/last/lastal/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { LAST_LASTAL } from '../../../../modules/nf-core/last/lastal/main.nf' workflow test_last_lastal_with_dummy_param_file { diff --git a/tests/modules/nf-core/last/lastdb/main.nf b/tests/modules/nf-core/last/lastdb/main.nf index d1c7b79acb0..db1c166f3a7 100644 --- a/tests/modules/nf-core/last/lastdb/main.nf +++ b/tests/modules/nf-core/last/lastdb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_LASTDB } from '../../../../modules/last/lastdb/main.nf' +include { LAST_LASTDB } from '../../../../modules/nf-core/last/lastdb/main.nf' workflow test_last_lastdb { diff --git a/tests/modules/nf-core/last/mafconvert/main.nf b/tests/modules/nf-core/last/mafconvert/main.nf index c87f6e6aa28..f99b4c468f5 100644 --- a/tests/modules/nf-core/last/mafconvert/main.nf +++ b/tests/modules/nf-core/last/mafconvert/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_MAFCONVERT } from '../../../../modules/last/mafconvert/main.nf' +include { LAST_MAFCONVERT } from '../../../../modules/nf-core/last/mafconvert/main.nf' workflow test_last_mafconvert { diff --git a/tests/modules/nf-core/last/mafswap/main.nf b/tests/modules/nf-core/last/mafswap/main.nf index 5cc94932347..267ae0664e0 100644 --- a/tests/modules/nf-core/last/mafswap/main.nf +++ b/tests/modules/nf-core/last/mafswap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_MAFSWAP } from '../../../../modules/last/mafswap/main.nf' +include { LAST_MAFSWAP } from '../../../../modules/nf-core/last/mafswap/main.nf' workflow test_last_mafswap { diff --git a/tests/modules/nf-core/last/postmask/main.nf b/tests/modules/nf-core/last/postmask/main.nf index 9bbb10e9fa2..7de628ce610 100644 --- a/tests/modules/nf-core/last/postmask/main.nf +++ b/tests/modules/nf-core/last/postmask/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_POSTMASK } from '../../../../modules/last/postmask/main.nf' +include { LAST_POSTMASK } from '../../../../modules/nf-core/last/postmask/main.nf' workflow test_last_postmask { diff --git a/tests/modules/nf-core/last/split/main.nf b/tests/modules/nf-core/last/split/main.nf index f4ece4f21ef..c48fda38aa4 100644 --- a/tests/modules/nf-core/last/split/main.nf +++ b/tests/modules/nf-core/last/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_SPLIT } from '../../../../modules/last/split/main.nf' +include { LAST_SPLIT } from '../../../../modules/nf-core/last/split/main.nf' workflow test_last_split { diff --git a/tests/modules/nf-core/last/train/main.nf b/tests/modules/nf-core/last/train/main.nf index 2e10735e34f..dc1daa32fb7 100644 --- a/tests/modules/nf-core/last/train/main.nf +++ b/tests/modules/nf-core/last/train/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { LAST_TRAIN } from '../../../../modules/last/train/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { LAST_TRAIN } from '../../../../modules/nf-core/last/train/main.nf' workflow test_last_train { diff --git a/tests/modules/nf-core/leehom/main.nf b/tests/modules/nf-core/leehom/main.nf index 1615d2e14b0..8c0326a12a6 100644 --- a/tests/modules/nf-core/leehom/main.nf +++ b/tests/modules/nf-core/leehom/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { LEEHOM } from '../../../modules/leehom/main.nf' -include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf' +include { LEEHOM } from '../../../modules/nf-core/leehom/main.nf' +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main.nf' workflow test_leehom_bam { diff --git a/tests/modules/nf-core/legsta/main.nf b/tests/modules/nf-core/legsta/main.nf index 606d8209548..6bf4588cd79 100644 --- a/tests/modules/nf-core/legsta/main.nf +++ b/tests/modules/nf-core/legsta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LEGSTA } from '../../../modules/legsta/main.nf' +include { LEGSTA } from '../../../modules/nf-core/legsta/main.nf' workflow test_legsta { diff --git a/tests/modules/nf-core/lima/main.nf b/tests/modules/nf-core/lima/main.nf index 7501def9d32..7b716fa5be3 100644 --- a/tests/modules/nf-core/lima/main.nf +++ b/tests/modules/nf-core/lima/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LIMA } from '../../../modules/lima/main.nf' +include { LIMA } from '../../../modules/nf-core/lima/main.nf' workflow test_lima_bam { diff --git a/tests/modules/nf-core/lissero/main.nf b/tests/modules/nf-core/lissero/main.nf index 339576c34d9..712f6161e01 100644 --- a/tests/modules/nf-core/lissero/main.nf +++ b/tests/modules/nf-core/lissero/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LISSERO } from '../../../modules/lissero/main.nf' +include { LISSERO } from '../../../modules/nf-core/lissero/main.nf' workflow test_lissero { diff --git a/tests/modules/nf-core/lofreq/call/main.nf b/tests/modules/nf-core/lofreq/call/main.nf index 70da4ea59d2..d00e98a7592 100644 --- a/tests/modules/nf-core/lofreq/call/main.nf +++ b/tests/modules/nf-core/lofreq/call/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_CALL } from '../../../../modules/lofreq/call/main.nf' +include { LOFREQ_CALL } from '../../../../modules/nf-core/lofreq/call/main.nf' workflow test_lofreq_call { diff --git a/tests/modules/nf-core/lofreq/callparallel/main.nf b/tests/modules/nf-core/lofreq/callparallel/main.nf index 24ab2db3ba6..cae4505e8cb 100644 --- a/tests/modules/nf-core/lofreq/callparallel/main.nf +++ b/tests/modules/nf-core/lofreq/callparallel/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_CALLPARALLEL } from '../../../../modules/lofreq/callparallel/main.nf' +include { LOFREQ_CALLPARALLEL } from '../../../../modules/nf-core/lofreq/callparallel/main.nf' workflow test_lofreq_callparallel { diff --git a/tests/modules/nf-core/lofreq/filter/main.nf b/tests/modules/nf-core/lofreq/filter/main.nf index bd2a7f54fac..db2b5fd03c8 100644 --- a/tests/modules/nf-core/lofreq/filter/main.nf +++ b/tests/modules/nf-core/lofreq/filter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_FILTER } from '../../../../modules/lofreq/filter/main.nf' +include { LOFREQ_FILTER } from '../../../../modules/nf-core/lofreq/filter/main.nf' workflow test_lofreq_filter { diff --git a/tests/modules/nf-core/lofreq/indelqual/main.nf b/tests/modules/nf-core/lofreq/indelqual/main.nf index 71652ce14b1..c8b69b94c7d 100644 --- a/tests/modules/nf-core/lofreq/indelqual/main.nf +++ b/tests/modules/nf-core/lofreq/indelqual/main.nf @@ -3,7 +3,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_INDELQUAL } from '../../../../modules/lofreq/indelqual/main.nf' +include { LOFREQ_INDELQUAL } from '../../../../modules/nf-core/lofreq/indelqual/main.nf' workflow test_lofreq_indelqual { diff --git a/tests/modules/nf-core/macrel/contigs/main.nf b/tests/modules/nf-core/macrel/contigs/main.nf index a613dcc42c9..986a1a20e34 100644 --- a/tests/modules/nf-core/macrel/contigs/main.nf +++ b/tests/modules/nf-core/macrel/contigs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MACREL_CONTIGS } from '../../../../modules/macrel/contigs/main.nf' +include { MACREL_CONTIGS } from '../../../../modules/nf-core/macrel/contigs/main.nf' workflow test_macrel_contigs { diff --git a/tests/modules/nf-core/macs2/callpeak/main.nf b/tests/modules/nf-core/macs2/callpeak/main.nf index 070469dd329..a65675b5c80 100644 --- a/tests/modules/nf-core/macs2/callpeak/main.nf +++ b/tests/modules/nf-core/macs2/callpeak/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf' -include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/macs2/callpeak/main.nf' -include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/macs2/callpeak/main.nf' +include { MACS2_CALLPEAK } from '../../../../modules/nf-core/macs2/callpeak/main.nf' +include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/nf-core/macs2/callpeak/main.nf' +include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/nf-core/macs2/callpeak/main.nf' workflow test_macs2_callpeak_bed { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/mafft/main.nf b/tests/modules/nf-core/mafft/main.nf index 7f50b35aef9..ee91863f6c1 100644 --- a/tests/modules/nf-core/mafft/main.nf +++ b/tests/modules/nf-core/mafft/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAFFT } from '../../../modules/mafft/main.nf' +include { MAFFT } from '../../../modules/nf-core/mafft/main.nf' workflow test_mafft { diff --git a/tests/modules/nf-core/malt/build_test/main.nf b/tests/modules/nf-core/malt/build_test/main.nf index 6b8de805bb5..95d01942edc 100644 --- a/tests/modules/nf-core/malt/build_test/main.nf +++ b/tests/modules/nf-core/malt/build_test/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNZIP } from '../../../../modules/unzip/main.nf' -include { MALT_BUILD } from '../../../../modules/malt/build/main.nf' +include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../../modules/nf-core/malt/build/main.nf' workflow test_malt_build { fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/malt/run/main.nf b/tests/modules/nf-core/malt/run/main.nf index 28db0e92f8a..85cee2c879d 100644 --- a/tests/modules/nf-core/malt/run/main.nf +++ b/tests/modules/nf-core/malt/run/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNZIP } from '../../../../modules/unzip/main.nf' -include { MALT_BUILD } from '../../../../modules/malt/build/main.nf' -include { MALT_RUN } from '../../../../modules/malt/run/main.nf' +include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../../modules/nf-core/malt/build/main.nf' +include { MALT_RUN } from '../../../../modules/nf-core/malt/run/main.nf' workflow test_malt_run { diff --git a/tests/modules/nf-core/maltextract/main.nf b/tests/modules/nf-core/maltextract/main.nf index ed1e32c9b38..88b889e4481 100644 --- a/tests/modules/nf-core/maltextract/main.nf +++ b/tests/modules/nf-core/maltextract/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf' -include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf' -include { MALT_BUILD } from '../../../modules/malt/build/main.nf' -include { MALT_RUN } from '../../../modules/malt/run/main.nf' -include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' +include { UNZIP as UNZIP_MALT } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../modules/nf-core/malt/build/main.nf' +include { MALT_RUN } from '../../../modules/nf-core/malt/run/main.nf' +include { MALTEXTRACT } from '../../../modules/nf-core/maltextract/main.nf' workflow test_maltextract { diff --git a/tests/modules/nf-core/manta/convertinversion/main.nf b/tests/modules/nf-core/manta/convertinversion/main.nf index 6997b5c9cf9..0ad19c74686 100644 --- a/tests/modules/nf-core/manta/convertinversion/main.nf +++ b/tests/modules/nf-core/manta/convertinversion/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MANTA_CONVERTINVERSION } from '../../../../modules/manta/convertinversion/main.nf' -include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf' +include { MANTA_CONVERTINVERSION } from '../../../../modules/nf-core/manta/convertinversion/main.nf' +include { MANTA_TUMORONLY } from '../../../../modules/nf-core/manta/tumoronly/main.nf' workflow test_manta_convertinversion { diff --git a/tests/modules/nf-core/manta/germline/main.nf b/tests/modules/nf-core/manta/germline/main.nf index 5f6687b2749..5bc0476d558 100644 --- a/tests/modules/nf-core/manta/germline/main.nf +++ b/tests/modules/nf-core/manta/germline/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf' +include { MANTA_GERMLINE } from '../../../../modules/nf-core/manta/germline/main.nf' workflow test_manta_germline { input = [ diff --git a/tests/modules/nf-core/manta/somatic/main.nf b/tests/modules/nf-core/manta/somatic/main.nf index b32a273ef69..71bca3101af 100644 --- a/tests/modules/nf-core/manta/somatic/main.nf +++ b/tests/modules/nf-core/manta/somatic/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MANTA_SOMATIC } from '../../../../modules/manta/somatic/main.nf' +include { MANTA_SOMATIC } from '../../../../modules/nf-core/manta/somatic/main.nf' workflow test_manta_somatic { diff --git a/tests/modules/nf-core/manta/tumoronly/main.nf b/tests/modules/nf-core/manta/tumoronly/main.nf index dbe079140e4..e120048c2f2 100644 --- a/tests/modules/nf-core/manta/tumoronly/main.nf +++ b/tests/modules/nf-core/manta/tumoronly/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf' +include { MANTA_TUMORONLY } from '../../../../modules/nf-core/manta/tumoronly/main.nf' workflow test_manta_tumoronly { input = [ diff --git a/tests/modules/nf-core/mapdamage2/main.nf b/tests/modules/nf-core/mapdamage2/main.nf index b7e4d23b06e..105f24dec80 100644 --- a/tests/modules/nf-core/mapdamage2/main.nf +++ b/tests/modules/nf-core/mapdamage2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAPDAMAGE2 } from '../../../modules/mapdamage2/main.nf' +include { MAPDAMAGE2 } from '../../../modules/nf-core/mapdamage2/main.nf' workflow test_mapdamage2 { diff --git a/tests/modules/nf-core/mash/dist/main.nf b/tests/modules/nf-core/mash/dist/main.nf index 10c9c9fa3c3..75a01e0ace0 100644 --- a/tests/modules/nf-core/mash/dist/main.nf +++ b/tests/modules/nf-core/mash/dist/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MASH_DIST } from '../../../../modules/mash/dist/main.nf' +include { MASH_DIST } from '../../../../modules/nf-core/mash/dist/main.nf' workflow test_mash_dist { diff --git a/tests/modules/nf-core/mash/screen/main.nf b/tests/modules/nf-core/mash/screen/main.nf index 5338d932ee8..40345d57017 100644 --- a/tests/modules/nf-core/mash/screen/main.nf +++ b/tests/modules/nf-core/mash/screen/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MASH_SKETCH } from '../../../../modules/mash/sketch/main.nf' -include { MASH_SCREEN } from '../../../../modules/mash/screen/main.nf' +include { MASH_SKETCH } from '../../../../modules/nf-core/mash/sketch/main.nf' +include { MASH_SCREEN } from '../../../../modules/nf-core/mash/screen/main.nf' workflow test_mash_screen { diff --git a/tests/modules/nf-core/mash/sketch/main.nf b/tests/modules/nf-core/mash/sketch/main.nf index cec2035b704..5a95895876c 100644 --- a/tests/modules/nf-core/mash/sketch/main.nf +++ b/tests/modules/nf-core/mash/sketch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MASH_SKETCH } from '../../../../modules/mash/sketch/main.nf' +include { MASH_SKETCH } from '../../../../modules/nf-core/mash/sketch/main.nf' workflow test_mash_sketch { diff --git a/tests/modules/nf-core/mashtree/main.nf b/tests/modules/nf-core/mashtree/main.nf index 07f5e561f1e..63a03887c70 100644 --- a/tests/modules/nf-core/mashtree/main.nf +++ b/tests/modules/nf-core/mashtree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MASHTREE } from '../../../modules/mashtree/main.nf' +include { MASHTREE } from '../../../modules/nf-core/mashtree/main.nf' workflow test_mashtree { diff --git a/tests/modules/nf-core/maxbin2/main.nf b/tests/modules/nf-core/maxbin2/main.nf index 3df417be3de..d6d5d2c4988 100644 --- a/tests/modules/nf-core/maxbin2/main.nf +++ b/tests/modules/nf-core/maxbin2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAXBIN2 } from '../../../modules/maxbin2/main.nf' +include { MAXBIN2 } from '../../../modules/nf-core/maxbin2/main.nf' workflow test_maxbin2 { diff --git a/tests/modules/nf-core/maxquant/lfq/main.nf b/tests/modules/nf-core/maxquant/lfq/main.nf index bb9b7976a59..ee1c92ae33a 100644 --- a/tests/modules/nf-core/maxquant/lfq/main.nf +++ b/tests/modules/nf-core/maxquant/lfq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] ) +include { MAXQUANT_LFQ } from '../../../../modules/nf-core/maxquant/lfq/main.nf' addParams( options: [:] ) workflow test_maxquant_lfq { diff --git a/tests/modules/nf-core/mcroni/main.nf b/tests/modules/nf-core/mcroni/main.nf index 6ef0dd49c60..bd11b702822 100644 --- a/tests/modules/nf-core/mcroni/main.nf +++ b/tests/modules/nf-core/mcroni/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MCRONI } from '../../../modules/mcroni/main.nf' +include { MCRONI } from '../../../modules/nf-core/mcroni/main.nf' workflow test_mcroni { diff --git a/tests/modules/nf-core/md5sum/main.nf b/tests/modules/nf-core/md5sum/main.nf index f90642b6e4c..1995b2a921d 100644 --- a/tests/modules/nf-core/md5sum/main.nf +++ b/tests/modules/nf-core/md5sum/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MD5SUM } from '../../../modules/md5sum/main.nf' +include { MD5SUM } from '../../../modules/nf-core/md5sum/main.nf' workflow test_md5sum { diff --git a/tests/modules/nf-core/medaka/main.nf b/tests/modules/nf-core/medaka/main.nf index 75fc135b422..4fe483d009f 100644 --- a/tests/modules/nf-core/medaka/main.nf +++ b/tests/modules/nf-core/medaka/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MEDAKA } from '../../../modules/medaka/main.nf' +include { MEDAKA } from '../../../modules/nf-core/medaka/main.nf' workflow test_medaka { diff --git a/tests/modules/nf-core/megahit/main.nf b/tests/modules/nf-core/megahit/main.nf index 88acf3e3706..78b0fc49cca 100644 --- a/tests/modules/nf-core/megahit/main.nf +++ b/tests/modules/nf-core/megahit/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MEGAHIT } from '../../../modules/megahit/main.nf' +include { MEGAHIT } from '../../../modules/nf-core/megahit/main.nf' workflow test_megahit { diff --git a/tests/modules/nf-core/megan/daa2info/main.nf b/tests/modules/nf-core/megan/daa2info/main.nf index 840a14a26b2..2ea860a8c37 100644 --- a/tests/modules/nf-core/megan/daa2info/main.nf +++ b/tests/modules/nf-core/megan/daa2info/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' -include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf' -include { MEGAN_DAA2INFO } from '../../../../modules/megan/daa2info/main.nf' +include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_BLASTX } from '../../../../modules/nf-core/diamond/blastx/main.nf' +include { MEGAN_DAA2INFO } from '../../../../modules/nf-core/megan/daa2info/main.nf' workflow test_megan_daa2info { diff --git a/tests/modules/nf-core/megan/rma2info/main.nf b/tests/modules/nf-core/megan/rma2info/main.nf index edbe9a4909b..7b78ae5b089 100644 --- a/tests/modules/nf-core/megan/rma2info/main.nf +++ b/tests/modules/nf-core/megan/rma2info/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MEGAN_RMA2INFO } from '../../../../modules/megan/rma2info/main.nf' +include { MEGAN_RMA2INFO } from '../../../../modules/nf-core/megan/rma2info/main.nf' workflow test_megan_rma2info { diff --git a/tests/modules/nf-core/meningotype/main.nf b/tests/modules/nf-core/meningotype/main.nf index a2d0ff10f46..eeee73c3247 100644 --- a/tests/modules/nf-core/meningotype/main.nf +++ b/tests/modules/nf-core/meningotype/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MENINGOTYPE } from '../../../modules/meningotype/main.nf' +include { MENINGOTYPE } from '../../../modules/nf-core/meningotype/main.nf' workflow test_meningotype { diff --git a/tests/modules/nf-core/merqury/main.nf b/tests/modules/nf-core/merqury/main.nf index 9a12294bb7c..c453ed28c75 100644 --- a/tests/modules/nf-core/merqury/main.nf +++ b/tests/modules/nf-core/merqury/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../modules/meryl/count/main.nf' -include { MERYL_UNIONSUM } from '../../../modules/meryl/unionsum/main.nf' -include { MERQURY } from '../../../modules/merqury/main.nf' +include { MERYL_COUNT } from '../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_UNIONSUM } from '../../../modules/nf-core/meryl/unionsum/main.nf' +include { MERQURY } from '../../../modules/nf-core/merqury/main.nf' workflow test_merqury { diff --git a/tests/modules/nf-core/merquryfk/katcomp/main.nf b/tests/modules/nf-core/merquryfk/katcomp/main.nf index 74d9a3ea2c9..32c2f68a70d 100644 --- a/tests/modules/nf-core/merquryfk/katcomp/main.nf +++ b/tests/modules/nf-core/merquryfk/katcomp/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK as FASTK1 } from '../../../../modules/fastk/fastk/main.nf' -include { FASTK_FASTK as FASTK2 } from '../../../../modules/fastk/fastk/main.nf' -include { MERQURYFK_KATCOMP } from '../../../../modules/merquryfk/katcomp/main.nf' +include { FASTK_FASTK as FASTK1 } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_FASTK as FASTK2 } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_KATCOMP } from '../../../../modules/nf-core/merquryfk/katcomp/main.nf' workflow test_merquryfk_katcomp_png { diff --git a/tests/modules/nf-core/merquryfk/katgc/main.nf b/tests/modules/nf-core/merquryfk/katgc/main.nf index 4dbefab4568..a398f991279 100644 --- a/tests/modules/nf-core/merquryfk/katgc/main.nf +++ b/tests/modules/nf-core/merquryfk/katgc/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf' -include { MERQURYFK_KATGC } from '../../../../modules/merquryfk/katgc/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_KATGC } from '../../../../modules/nf-core/merquryfk/katgc/main.nf' workflow test_merquryfk_katgc_png { diff --git a/tests/modules/nf-core/merquryfk/merquryfk/main.nf b/tests/modules/nf-core/merquryfk/merquryfk/main.nf index 99280374911..4c08f12055c 100644 --- a/tests/modules/nf-core/merquryfk/merquryfk/main.nf +++ b/tests/modules/nf-core/merquryfk/merquryfk/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf' -include { MERQURYFK_MERQURYFK } from '../../../../modules/merquryfk/merquryfk/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_MERQURYFK } from '../../../../modules/nf-core/merquryfk/merquryfk/main.nf' workflow test_merquryfk_merquryfk_png { diff --git a/tests/modules/nf-core/merquryfk/ploidyplot/main.nf b/tests/modules/nf-core/merquryfk/ploidyplot/main.nf index df582b98841..a9d52dd072c 100644 --- a/tests/modules/nf-core/merquryfk/ploidyplot/main.nf +++ b/tests/modules/nf-core/merquryfk/ploidyplot/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf' -include { MERQURYFK_PLOIDYPLOT } from '../../../../modules/merquryfk/ploidyplot/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_PLOIDYPLOT } from '../../../../modules/nf-core/merquryfk/ploidyplot/main.nf' workflow test_merquryfk_ploidyplot_png { diff --git a/tests/modules/nf-core/meryl/count/main.nf b/tests/modules/nf-core/meryl/count/main.nf index 3c9a64c7ede..efd03eabd9c 100644 --- a/tests/modules/nf-core/meryl/count/main.nf +++ b/tests/modules/nf-core/meryl/count/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf' +include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' workflow test_meryl_count_single_end { diff --git a/tests/modules/nf-core/meryl/histogram/main.nf b/tests/modules/nf-core/meryl/histogram/main.nf index 697a12efe1c..57f6ebd7e6f 100644 --- a/tests/modules/nf-core/meryl/histogram/main.nf +++ b/tests/modules/nf-core/meryl/histogram/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf' -include { MERYL_HISTOGRAM } from '../../../../modules/meryl/histogram/main.nf' +include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_HISTOGRAM } from '../../../../modules/nf-core/meryl/histogram/main.nf' workflow test_meryl_histogram { diff --git a/tests/modules/nf-core/meryl/unionsum/main.nf b/tests/modules/nf-core/meryl/unionsum/main.nf index 6dd40c82317..cb3e13cb461 100644 --- a/tests/modules/nf-core/meryl/unionsum/main.nf +++ b/tests/modules/nf-core/meryl/unionsum/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf' -include { MERYL_UNIONSUM } from '../../../../modules/meryl/unionsum/main.nf' +include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_UNIONSUM } from '../../../../modules/nf-core/meryl/unionsum/main.nf' workflow test_meryl_unionsum_single_end { diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 00309402134..1b67b1505f7 100644 --- a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' workflow test_metabat2_jgisummarizebamcontigdepths { diff --git a/tests/modules/nf-core/metabat2/metabat2/main.nf b/tests/modules/nf-core/metabat2/metabat2/main.nf index 0179e4c37ab..0122881926e 100644 --- a/tests/modules/nf-core/metabat2/metabat2/main.nf +++ b/tests/modules/nf-core/metabat2/metabat2/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' +include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' workflow test_metabat2_no_depth { diff --git a/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index 6a158d6ae2f..fa8695e0e92 100644 --- a/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { METAPHLAN3 } from '../../../../modules/metaphlan3/metaphlan3/main.nf' -include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../modules/metaphlan3/mergemetaphlantables/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { METAPHLAN3 } from '../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf' +include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../modules/nf-core/metaphlan3/mergemetaphlantables/main.nf' workflow test_metaphlan3_mergemetaphlantables { diff --git a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf index 524936ae9d5..cfba3b2dce4 100644 --- a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { METAPHLAN3_METAPHLAN3 } from '../../../../modules/metaphlan3/metaphlan3/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { METAPHLAN3_METAPHLAN3 } from '../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf' workflow test_metaphlan3_single_end { diff --git a/tests/modules/nf-core/methyldackel/extract/main.nf b/tests/modules/nf-core/methyldackel/extract/main.nf index 92f923087d9..499cac4bb77 100644 --- a/tests/modules/nf-core/methyldackel/extract/main.nf +++ b/tests/modules/nf-core/methyldackel/extract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { METHYLDACKEL_EXTRACT } from '../../../../modules/methyldackel/extract/main.nf' +include { METHYLDACKEL_EXTRACT } from '../../../../modules/nf-core/methyldackel/extract/main.nf' workflow test_methyldackel_extract { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/methyldackel/mbias/main.nf b/tests/modules/nf-core/methyldackel/mbias/main.nf index f304e22fb08..99e5f1dfede 100644 --- a/tests/modules/nf-core/methyldackel/mbias/main.nf +++ b/tests/modules/nf-core/methyldackel/mbias/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { METHYLDACKEL_MBIAS } from '../../../../modules/methyldackel/mbias/main.nf' +include { METHYLDACKEL_MBIAS } from '../../../../modules/nf-core/methyldackel/mbias/main.nf' workflow test_methyldackel_mbias { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/minia/main.nf b/tests/modules/nf-core/minia/main.nf index 5be4d17f129..659f4dec787 100644 --- a/tests/modules/nf-core/minia/main.nf +++ b/tests/modules/nf-core/minia/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIA } from '../../../modules/minia/main.nf' +include { MINIA } from '../../../modules/nf-core/minia/main.nf' workflow test_minia { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/miniasm/main.nf b/tests/modules/nf-core/miniasm/main.nf index 949660acb9d..bbb6bffc0bb 100644 --- a/tests/modules/nf-core/miniasm/main.nf +++ b/tests/modules/nf-core/miniasm/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIASM } from '../../../modules/miniasm/main.nf' +include { MINIASM } from '../../../modules/nf-core/miniasm/main.nf' workflow test_miniasm { diff --git a/tests/modules/nf-core/minimap2/align/main.nf b/tests/modules/nf-core/minimap2/align/main.nf index ee6c083885c..6866ad349a1 100644 --- a/tests/modules/nf-core/minimap2/align/main.nf +++ b/tests/modules/nf-core/minimap2/align/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIMAP2_ALIGN } from '../../../../modules/minimap2/align/main.nf' +include { MINIMAP2_ALIGN } from '../../../../modules/nf-core/minimap2/align/main.nf' workflow test_minimap2_align_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/minimap2/index/main.nf b/tests/modules/nf-core/minimap2/index/main.nf index 8eb515696d5..ac0dabc4964 100644 --- a/tests/modules/nf-core/minimap2/index/main.nf +++ b/tests/modules/nf-core/minimap2/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIMAP2_INDEX } from '../../../../modules/minimap2/index/main.nf' +include { MINIMAP2_INDEX } from '../../../../modules/nf-core/minimap2/index/main.nf' workflow test_minimap2_index { diff --git a/tests/modules/nf-core/mlst/main.nf b/tests/modules/nf-core/mlst/main.nf index f84ec622dee..d924d06a707 100644 --- a/tests/modules/nf-core/mlst/main.nf +++ b/tests/modules/nf-core/mlst/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MLST } from '../../../modules/mlst/main.nf' +include { MLST } from '../../../modules/nf-core/mlst/main.nf' workflow test_mlst { diff --git a/tests/modules/nf-core/mobsuite/recon/main.nf b/tests/modules/nf-core/mobsuite/recon/main.nf index 0d18ef9cd51..eb53a20bf97 100644 --- a/tests/modules/nf-core/mobsuite/recon/main.nf +++ b/tests/modules/nf-core/mobsuite/recon/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MOBSUITE_RECON } from '../../../../modules/mobsuite/recon/main.nf' +include { MOBSUITE_RECON } from '../../../../modules/nf-core/mobsuite/recon/main.nf' workflow test_mobsuite_recon { diff --git a/tests/modules/nf-core/mosdepth/main.nf b/tests/modules/nf-core/mosdepth/main.nf index 1bb8e8ff5cf..20797307277 100644 --- a/tests/modules/nf-core/mosdepth/main.nf +++ b/tests/modules/nf-core/mosdepth/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../modules/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/mosdepth/main.nf' +include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/nf-core/mosdepth/main.nf' workflow test_mosdepth { input = [ diff --git a/tests/modules/nf-core/motus/downloaddb/main.nf b/tests/modules/nf-core/motus/downloaddb/main.nf index f7680ca953f..328d957e506 100644 --- a/tests/modules/nf-core/motus/downloaddb/main.nf +++ b/tests/modules/nf-core/motus/downloaddb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf' +include { MOTUS_DOWNLOADDB } from '../../../../modules/nf-core/motus/downloaddb/main.nf' workflow test_motus_downloaddb { diff --git a/tests/modules/nf-core/motus/merge/main.nf b/tests/modules/nf-core/motus/merge/main.nf index bb1b71500e7..d46546e71c8 100644 --- a/tests/modules/nf-core/motus/merge/main.nf +++ b/tests/modules/nf-core/motus/merge/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf' -include { MOTUS_PROFILE } from '../../../../modules/motus/profile/main.nf' -include { MOTUS_MERGE } from '../../../../modules/motus/merge/main.nf' -include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../modules/motus/merge/main.nf' +include { MOTUS_DOWNLOADDB } from '../../../../modules/nf-core/motus/downloaddb/main.nf' +include { MOTUS_PROFILE } from '../../../../modules/nf-core/motus/profile/main.nf' +include { MOTUS_MERGE } from '../../../../modules/nf-core/motus/merge/main.nf' +include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../modules/nf-core/motus/merge/main.nf' workflow test_motus_merge { diff --git a/tests/modules/nf-core/motus/profile/main.nf b/tests/modules/nf-core/motus/profile/main.nf index 068ef6cfde1..8c1eb873561 100644 --- a/tests/modules/nf-core/motus/profile/main.nf +++ b/tests/modules/nf-core/motus/profile/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf' -include { MOTUS_PROFILE } from '../../../../modules/motus/profile/main.nf' +include { MOTUS_DOWNLOADDB } from '../../../../modules/nf-core/motus/downloaddb/main.nf' +include { MOTUS_PROFILE } from '../../../../modules/nf-core/motus/profile/main.nf' workflow test_motus_profile_single_end { diff --git a/tests/modules/nf-core/msisensor/msi/main.nf b/tests/modules/nf-core/msisensor/msi/main.nf index 259ec8870fb..4be59d25ea8 100644 --- a/tests/modules/nf-core/msisensor/msi/main.nf +++ b/tests/modules/nf-core/msisensor/msi/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf' -include { MSISENSOR_MSI } from '../../../../modules/msisensor/msi/main.nf' +include { MSISENSOR_SCAN } from '../../../../modules/nf-core/msisensor/scan/main.nf' +include { MSISENSOR_MSI } from '../../../../modules/nf-core/msisensor/msi/main.nf' workflow test_msisensor_msi { diff --git a/tests/modules/nf-core/msisensor/scan/main.nf b/tests/modules/nf-core/msisensor/scan/main.nf index de46dd9b524..2fb73c705a1 100644 --- a/tests/modules/nf-core/msisensor/scan/main.nf +++ b/tests/modules/nf-core/msisensor/scan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf' +include { MSISENSOR_SCAN } from '../../../../modules/nf-core/msisensor/scan/main.nf' workflow test_msisensor_scan { diff --git a/tests/modules/nf-core/msisensor2/msi/main.nf b/tests/modules/nf-core/msisensor2/msi/main.nf index 6105af62bbd..0c5b335f249 100644 --- a/tests/modules/nf-core/msisensor2/msi/main.nf +++ b/tests/modules/nf-core/msisensor2/msi/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MSISENSOR2_SCAN } from '../../../../modules/msisensor2/scan/main.nf' -include { MSISENSOR2_MSI } from '../../../../modules/msisensor2/msi/main.nf' +include { MSISENSOR2_SCAN } from '../../../../modules/nf-core/msisensor2/scan/main.nf' +include { MSISENSOR2_MSI } from '../../../../modules/nf-core/msisensor2/msi/main.nf' workflow test_msisensor2_msi_tumor_only { diff --git a/tests/modules/nf-core/msisensor2/scan/main.nf b/tests/modules/nf-core/msisensor2/scan/main.nf index 52a600bd5fc..2f92f82c5d3 100644 --- a/tests/modules/nf-core/msisensor2/scan/main.nf +++ b/tests/modules/nf-core/msisensor2/scan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MSISENSOR2_SCAN } from '../../../../modules/msisensor2/scan/main.nf' +include { MSISENSOR2_SCAN } from '../../../../modules/nf-core/msisensor2/scan/main.nf' workflow test_msisensor2_scan { diff --git a/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf b/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf index 4516ada583f..8a78998f7c8 100644 --- a/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MSISENSORPRO_MSI_SOMATIC } from '../../../../modules/msisensorpro/msi_somatic/main.nf' -include { MSISENSORPRO_SCAN } from '../../../../modules/msisensorpro/scan/main.nf' +include { MSISENSORPRO_MSI_SOMATIC } from '../../../../modules/nf-core/msisensorpro/msi_somatic/main.nf' +include { MSISENSORPRO_SCAN } from '../../../../modules/nf-core/msisensorpro/scan/main.nf' workflow test_msisensorpro_msi { diff --git a/tests/modules/nf-core/msisensorpro/scan/main.nf b/tests/modules/nf-core/msisensorpro/scan/main.nf index cf57b820f8e..8413c662806 100644 --- a/tests/modules/nf-core/msisensorpro/scan/main.nf +++ b/tests/modules/nf-core/msisensorpro/scan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MSISENSORPRO_SCAN } from '../../../../modules/msisensorpro/scan/main.nf' +include { MSISENSORPRO_SCAN } from '../../../../modules/nf-core/msisensorpro/scan/main.nf' workflow test_msisensorpro_scan { diff --git a/tests/modules/nf-core/mtnucratio/main.nf b/tests/modules/nf-core/mtnucratio/main.nf index 6d6f5e1d1ef..ee7d1572cb2 100644 --- a/tests/modules/nf-core/mtnucratio/main.nf +++ b/tests/modules/nf-core/mtnucratio/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MTNUCRATIO } from '../../../modules/mtnucratio/main.nf' +include { MTNUCRATIO } from '../../../modules/nf-core/mtnucratio/main.nf' workflow test_mtnucratio { diff --git a/tests/modules/nf-core/multiqc/main.nf b/tests/modules/nf-core/multiqc/main.nf index ee0edabc060..640240a0cb1 100644 --- a/tests/modules/nf-core/multiqc/main.nf +++ b/tests/modules/nf-core/multiqc/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTQC } from '../../../modules/fastqc/main.nf' -include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf' -include { MULTIQC } from '../../../modules/multiqc/main.nf' +include { FASTQC } from '../../../modules/nf-core/fastqc/main.nf' +include { FASTQC as FASTQC2 } from '../../../modules/nf-core/fastqc/main.nf' +include { MULTIQC } from '../../../modules/nf-core/multiqc/main.nf' workflow test_multiqc { input = [ diff --git a/tests/modules/nf-core/multivcfanalyzer/main.nf b/tests/modules/nf-core/multivcfanalyzer/main.nf index 07e6831bf13..92915fdc113 100644 --- a/tests/modules/nf-core/multivcfanalyzer/main.nf +++ b/tests/modules/nf-core/multivcfanalyzer/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK_UNIFIEDGENOTYPER } from '../../../modules/gatk/unifiedgenotyper/main.nf' -include { GUNZIP } from '../../../modules/gunzip/main.nf' -include { MULTIVCFANALYZER } from '../../../modules/multivcfanalyzer/main.nf' +include { GATK_UNIFIEDGENOTYPER } from '../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' +include { MULTIVCFANALYZER } from '../../../modules/nf-core/multivcfanalyzer/main.nf' workflow test_multivcfanalyzer { diff --git a/tests/modules/nf-core/mummer/main.nf b/tests/modules/nf-core/mummer/main.nf index 30c8c4b82a8..ce7bbc661b5 100644 --- a/tests/modules/nf-core/mummer/main.nf +++ b/tests/modules/nf-core/mummer/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MUMMER } from '../../../modules/mummer/main.nf' +include { MUMMER } from '../../../modules/nf-core/mummer/main.nf' workflow test_mummer { diff --git a/tests/modules/nf-core/muscle/main.nf b/tests/modules/nf-core/muscle/main.nf index a62945198e2..0655f90a203 100644 --- a/tests/modules/nf-core/muscle/main.nf +++ b/tests/modules/nf-core/muscle/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MUSCLE } from '../../../modules/muscle/main.nf' -include { MUSCLE as MUSCLE_TREE } from '../../../modules/muscle/main.nf' +include { MUSCLE } from '../../../modules/nf-core/muscle/main.nf' +include { MUSCLE as MUSCLE_TREE } from '../../../modules/nf-core/muscle/main.nf' workflow test_muscle { diff --git a/tests/modules/nf-core/mykrobe/predict/main.nf b/tests/modules/nf-core/mykrobe/predict/main.nf index 384add1e3e3..7c37a7532f6 100644 --- a/tests/modules/nf-core/mykrobe/predict/main.nf +++ b/tests/modules/nf-core/mykrobe/predict/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf' +include { MYKROBE_PREDICT } from '../../../../modules/nf-core/mykrobe/predict/main.nf' workflow test_mykrobe_predict { diff --git a/tests/modules/nf-core/nanolyse/main.nf b/tests/modules/nf-core/nanolyse/main.nf index 91013cd00fe..ef4cd33980d 100644 --- a/tests/modules/nf-core/nanolyse/main.nf +++ b/tests/modules/nf-core/nanolyse/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NANOLYSE } from '../../../modules/nanolyse/main.nf' +include { NANOLYSE } from '../../../modules/nf-core/nanolyse/main.nf' workflow test_nanolyse { input = [ diff --git a/tests/modules/nf-core/nanoplot/main.nf b/tests/modules/nf-core/nanoplot/main.nf index 04c923c2961..395854171d6 100644 --- a/tests/modules/nf-core/nanoplot/main.nf +++ b/tests/modules/nf-core/nanoplot/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NANOPLOT } from '../../../modules/nanoplot/main.nf' +include { NANOPLOT } from '../../../modules/nf-core/nanoplot/main.nf' workflow test_nanoplot_summary { def input = [] diff --git a/tests/modules/nf-core/ncbigenomedownload/main.nf b/tests/modules/nf-core/ncbigenomedownload/main.nf index 2447b97c7f4..cb32ad285e3 100644 --- a/tests/modules/nf-core/ncbigenomedownload/main.nf +++ b/tests/modules/nf-core/ncbigenomedownload/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NCBIGENOMEDOWNLOAD } from '../../../modules/ncbigenomedownload/main.nf' +include { NCBIGENOMEDOWNLOAD } from '../../../modules/nf-core/ncbigenomedownload/main.nf' workflow test_ncbigenomedownload { diff --git a/tests/modules/nf-core/nextclade/datasetget/main.nf b/tests/modules/nf-core/nextclade/datasetget/main.nf index 8f4fa87b1e1..4b1033f04ab 100644 --- a/tests/modules/nf-core/nextclade/datasetget/main.nf +++ b/tests/modules/nf-core/nextclade/datasetget/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NEXTCLADE_DATASETGET } from '../../../../modules/nextclade/datasetget/main.nf' +include { NEXTCLADE_DATASETGET } from '../../../../modules/nf-core/nextclade/datasetget/main.nf' workflow test_nextclade_datasetget { diff --git a/tests/modules/nf-core/nextclade/run/main.nf b/tests/modules/nf-core/nextclade/run/main.nf index ed674a0d42a..5288e4874d8 100644 --- a/tests/modules/nf-core/nextclade/run/main.nf +++ b/tests/modules/nf-core/nextclade/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { NEXTCLADE_DATASETGET } from '../../../../modules/nextclade/datasetget/main.nf' -include { NEXTCLADE_RUN } from '../../../../modules/nextclade/run/main.nf' +include { NEXTCLADE_DATASETGET } from '../../../../modules/nf-core/nextclade/datasetget/main.nf' +include { NEXTCLADE_RUN } from '../../../../modules/nf-core/nextclade/run/main.nf' workflow test_nextclade_run { diff --git a/tests/modules/nf-core/nextgenmap/main.nf b/tests/modules/nf-core/nextgenmap/main.nf index 450551debc9..d1ed609247c 100644 --- a/tests/modules/nf-core/nextgenmap/main.nf +++ b/tests/modules/nf-core/nextgenmap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NEXTGENMAP } from '../../../modules/nextgenmap/main.nf' +include { NEXTGENMAP } from '../../../modules/nf-core/nextgenmap/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/ngmaster/main.nf b/tests/modules/nf-core/ngmaster/main.nf index b23530bccab..b3b2f27da4a 100644 --- a/tests/modules/nf-core/ngmaster/main.nf +++ b/tests/modules/nf-core/ngmaster/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NGMASTER } from '../../../modules/ngmaster/main.nf' +include { NGMASTER } from '../../../modules/nf-core/ngmaster/main.nf' workflow test_ngmaster { diff --git a/tests/modules/nf-core/ngscheckmate/ncm/main.nf b/tests/modules/nf-core/ngscheckmate/ncm/main.nf index ab6a46392ba..9b7bddd7560 100644 --- a/tests/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/tests/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../modules/ngscheckmate/ncm/main.nf' -include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../modules/ngscheckmate/ncm/main.nf' +include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../modules/nf-core/ngscheckmate/ncm/main.nf' +include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../modules/nf-core/ngscheckmate/ncm/main.nf' -include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf' +include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/nf-core/bedtools/makewindows/main.nf' -include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf' -include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../modules/bcftools/mpileup/main.nf' +include { BCFTOOLS_MPILEUP } from '../../../../modules/nf-core/bcftools/mpileup/main.nf' +include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../modules/nf-core/bcftools/mpileup/main.nf' workflow test_ngscheckmate_ncm_bam { input = [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), diff --git a/tests/modules/nf-core/nucmer/main.nf b/tests/modules/nf-core/nucmer/main.nf index 98e74b07d19..df9d3aedbeb 100644 --- a/tests/modules/nf-core/nucmer/main.nf +++ b/tests/modules/nf-core/nucmer/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NUCMER } from '../../../modules/nucmer/main.nf' +include { NUCMER } from '../../../modules/nf-core/nucmer/main.nf' workflow test_nucmer { diff --git a/tests/modules/nf-core/optitype/main.nf b/tests/modules/nf-core/optitype/main.nf index 6ed14d96dcb..c1a31718ecd 100644 --- a/tests/modules/nf-core/optitype/main.nf +++ b/tests/modules/nf-core/optitype/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { OPTITYPE } from '../../../modules/optitype/main.nf' +include { OPTITYPE } from '../../../modules/nf-core/optitype/main.nf' workflow test_optitype { input = [ [ id:'test', seq_type:'dna' ], // meta map diff --git a/tests/modules/nf-core/pairix/main.nf b/tests/modules/nf-core/pairix/main.nf index 474bacbbf47..e54c90b2d40 100644 --- a/tests/modules/nf-core/pairix/main.nf +++ b/tests/modules/nf-core/pairix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRIX } from '../../../modules/pairix/main.nf' +include { PAIRIX } from '../../../modules/nf-core/pairix/main.nf' workflow test_pairix { diff --git a/tests/modules/nf-core/pairtools/dedup/main.nf b/tests/modules/nf-core/pairtools/dedup/main.nf index 28121526d83..5735be4f529 100644 --- a/tests/modules/nf-core/pairtools/dedup/main.nf +++ b/tests/modules/nf-core/pairtools/dedup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_DEDUP } from '../../../../modules/pairtools/dedup/main.nf' +include { PAIRTOOLS_DEDUP } from '../../../../modules/nf-core/pairtools/dedup/main.nf' workflow test_pairtools_dedup { diff --git a/tests/modules/nf-core/pairtools/flip/main.nf b/tests/modules/nf-core/pairtools/flip/main.nf index e4d740e2077..0c3994f5b07 100644 --- a/tests/modules/nf-core/pairtools/flip/main.nf +++ b/tests/modules/nf-core/pairtools/flip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_FLIP } from '../../../../modules/pairtools/flip/main.nf' +include { PAIRTOOLS_FLIP } from '../../../../modules/nf-core/pairtools/flip/main.nf' workflow test_pairtools_flip { diff --git a/tests/modules/nf-core/pairtools/parse/main.nf b/tests/modules/nf-core/pairtools/parse/main.nf index f006fd6aef1..2ff878698db 100644 --- a/tests/modules/nf-core/pairtools/parse/main.nf +++ b/tests/modules/nf-core/pairtools/parse/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_PARSE } from '../../../../modules/pairtools/parse/main.nf' +include { PAIRTOOLS_PARSE } from '../../../../modules/nf-core/pairtools/parse/main.nf' workflow test_pairtools_parse { diff --git a/tests/modules/nf-core/pairtools/restrict/main.nf b/tests/modules/nf-core/pairtools/restrict/main.nf index ae7e328b62f..ca36e9a45bb 100644 --- a/tests/modules/nf-core/pairtools/restrict/main.nf +++ b/tests/modules/nf-core/pairtools/restrict/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_RESTRICT } from '../../../../modules/pairtools/restrict/main.nf' +include { PAIRTOOLS_RESTRICT } from '../../../../modules/nf-core/pairtools/restrict/main.nf' workflow test_pairtools_restrict { diff --git a/tests/modules/nf-core/pairtools/select/main.nf b/tests/modules/nf-core/pairtools/select/main.nf index ff65cd95262..9b41bb74aa2 100644 --- a/tests/modules/nf-core/pairtools/select/main.nf +++ b/tests/modules/nf-core/pairtools/select/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_SELECT } from '../../../../modules/pairtools/select/main.nf' +include { PAIRTOOLS_SELECT } from '../../../../modules/nf-core/pairtools/select/main.nf' workflow test_pairtools_select { diff --git a/tests/modules/nf-core/pairtools/sort/main.nf b/tests/modules/nf-core/pairtools/sort/main.nf index 0e484c76f0e..a5b77ca85f8 100644 --- a/tests/modules/nf-core/pairtools/sort/main.nf +++ b/tests/modules/nf-core/pairtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_SORT } from '../../../../modules/pairtools/sort/main.nf' +include { PAIRTOOLS_SORT } from '../../../../modules/nf-core/pairtools/sort/main.nf' workflow test_pairtools_sort { diff --git a/tests/modules/nf-core/panaroo/run/main.nf b/tests/modules/nf-core/panaroo/run/main.nf index 1fab62eddf6..fb0899b7843 100644 --- a/tests/modules/nf-core/panaroo/run/main.nf +++ b/tests/modules/nf-core/panaroo/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PANAROO_RUN } from '../../../../modules/panaroo/run/main.nf' +include { PANAROO_RUN } from '../../../../modules/nf-core/panaroo/run/main.nf' workflow test_panaroo_run { diff --git a/tests/modules/nf-core/pangolin/main.nf b/tests/modules/nf-core/pangolin/main.nf index ab4aa4af4da..9ee1995f76f 100644 --- a/tests/modules/nf-core/pangolin/main.nf +++ b/tests/modules/nf-core/pangolin/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PANGOLIN } from '../../../modules/pangolin/main.nf' +include { PANGOLIN } from '../../../modules/nf-core/pangolin/main.nf' workflow test_pangolin { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/paraclu/main.nf b/tests/modules/nf-core/paraclu/main.nf index 3bd75dc066c..9f1ccf26f94 100644 --- a/tests/modules/nf-core/paraclu/main.nf +++ b/tests/modules/nf-core/paraclu/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PARACLU } from '../../../modules/paraclu/main.nf' +include { PARACLU } from '../../../modules/nf-core/paraclu/main.nf' workflow test_paraclu { diff --git a/tests/modules/nf-core/pasty/main.nf b/tests/modules/nf-core/pasty/main.nf index 2dc5ea98f49..582e15997ec 100644 --- a/tests/modules/nf-core/pasty/main.nf +++ b/tests/modules/nf-core/pasty/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PASTY } from '../../../modules/pasty/main.nf' +include { PASTY } from '../../../modules/nf-core/pasty/main.nf' workflow test_pasty { diff --git a/tests/modules/nf-core/pbbam/pbmerge/main.nf b/tests/modules/nf-core/pbbam/pbmerge/main.nf index 34ed33a622e..af6330936b1 100644 --- a/tests/modules/nf-core/pbbam/pbmerge/main.nf +++ b/tests/modules/nf-core/pbbam/pbmerge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PBBAM_PBMERGE } from '../../../../modules/pbbam/pbmerge/main.nf' +include { PBBAM_PBMERGE } from '../../../../modules/nf-core/pbbam/pbmerge/main.nf' workflow test_pbbam_pbmerge { diff --git a/tests/modules/nf-core/pbccs/main.nf b/tests/modules/nf-core/pbccs/main.nf index 91a2ab30113..be09774ce32 100644 --- a/tests/modules/nf-core/pbccs/main.nf +++ b/tests/modules/nf-core/pbccs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PBCCS } from '../../../modules/pbccs/main.nf' +include { PBCCS } from '../../../modules/nf-core/pbccs/main.nf' workflow test_pbccs { diff --git a/tests/modules/nf-core/pbptyper/main.nf b/tests/modules/nf-core/pbptyper/main.nf index ba4854301ff..706f5804ac2 100644 --- a/tests/modules/nf-core/pbptyper/main.nf +++ b/tests/modules/nf-core/pbptyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PBPTYPER } from '../../../modules/pbptyper/main.nf' +include { PBPTYPER } from '../../../modules/nf-core/pbptyper/main.nf' workflow test_pbptyper { diff --git a/tests/modules/nf-core/pear/main.nf b/tests/modules/nf-core/pear/main.nf index 3646740d301..f46e7789387 100644 --- a/tests/modules/nf-core/pear/main.nf +++ b/tests/modules/nf-core/pear/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PEAR } from '../../../modules/pear/main.nf' +include { PEAR } from '../../../modules/nf-core/pear/main.nf' workflow test_pear { diff --git a/tests/modules/nf-core/peddy/main.nf b/tests/modules/nf-core/peddy/main.nf index e53e8152122..41821768834 100644 --- a/tests/modules/nf-core/peddy/main.nf +++ b/tests/modules/nf-core/peddy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PEDDY } from '../../../modules/peddy/main.nf' +include { PEDDY } from '../../../modules/nf-core/peddy/main.nf' workflow test_peddy { diff --git a/tests/modules/nf-core/phantompeakqualtools/main.nf b/tests/modules/nf-core/phantompeakqualtools/main.nf index 3b995d68083..7d91e3f156c 100644 --- a/tests/modules/nf-core/phantompeakqualtools/main.nf +++ b/tests/modules/nf-core/phantompeakqualtools/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PHANTOMPEAKQUALTOOLS } from '../../../modules/phantompeakqualtools/main.nf' +include { PHANTOMPEAKQUALTOOLS } from '../../../modules/nf-core/phantompeakqualtools/main.nf' workflow test_phantompeakqualtools_single_end { diff --git a/tests/modules/nf-core/phyloflash/main.nf b/tests/modules/nf-core/phyloflash/main.nf index 412e0321fd7..18f2b1cae94 100644 --- a/tests/modules/nf-core/phyloflash/main.nf +++ b/tests/modules/nf-core/phyloflash/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PHYLOFLASH } from '../../../modules/phyloflash/main.nf' +include { PHYLOFLASH } from '../../../modules/nf-core/phyloflash/main.nf' process STUB_PHYLOFLASH_DATABASE { output: diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf index d5148c36817..71ae501d7fe 100644 --- a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../modules/picard/addorreplacereadgroups/main.nf' +include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../modules/nf-core/picard/addorreplacereadgroups/main.nf' workflow test_picard_addorreplacereadgroups { diff --git a/tests/modules/nf-core/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf index f189b0f3d20..c6f4a2d890b 100644 --- a/tests/modules/nf-core/picard/cleansam/main.nf +++ b/tests/modules/nf-core/picard/cleansam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_CLEANSAM } from '../../../../modules/picard/cleansam/main.nf' +include { PICARD_CLEANSAM } from '../../../../modules/nf-core/picard/cleansam/main.nf' workflow test_picard_cleansam { diff --git a/tests/modules/nf-core/picard/collecthsmetrics/main.nf b/tests/modules/nf-core/picard/collecthsmetrics/main.nf index b25f3bf576e..913d29e4621 100644 --- a/tests/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/tests/modules/nf-core/picard/collecthsmetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsmetrics/main.nf' +include { PICARD_COLLECTHSMETRICS } from '../../../../modules/nf-core/picard/collecthsmetrics/main.nf' workflow test_picard_collecthsmetrics { diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf index 3a103f65829..4eb7d63b708 100644 --- a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/nf-core/picard/collectmultiplemetrics/main.nf' workflow test_picard_collectmultiplemetrics { input = [ diff --git a/tests/modules/nf-core/picard/collectwgsmetrics/main.nf b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf index eddf56031fe..1e7fb9bff10 100644 --- a/tests/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgsmetrics/main.nf' +include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/nf-core/picard/collectwgsmetrics/main.nf' workflow test_picard_collectwgsmetrics { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/picard/createsequencedictionary/main.nf b/tests/modules/nf-core/picard/createsequencedictionary/main.nf index 4dc24c8a423..9a678467f9e 100644 --- a/tests/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/tests/modules/nf-core/picard/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../modules/picard/createsequencedictionary/main.nf' +include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../modules/nf-core/picard/createsequencedictionary/main.nf' workflow test_picard_createsequencedictionary { diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf index 55ddb5c5966..d7c21662fae 100644 --- a/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../modules/picard/crosscheckfingerprints/main.nf' +include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../modules/nf-core/picard/crosscheckfingerprints/main.nf' workflow test_picard_crosscheckfingerprints { diff --git a/tests/modules/nf-core/picard/fastqtosam/main.nf b/tests/modules/nf-core/picard/fastqtosam/main.nf index 2eb55e63995..e2b42ee53a9 100644 --- a/tests/modules/nf-core/picard/fastqtosam/main.nf +++ b/tests/modules/nf-core/picard/fastqtosam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_FASTQTOSAM } from '../../../../modules/picard/fastqtosam/main.nf' +include { PICARD_FASTQTOSAM } from '../../../../modules/nf-core/picard/fastqtosam/main.nf' workflow test_picard_fastqtosam_single { diff --git a/tests/modules/nf-core/picard/filtersamreads/main.nf b/tests/modules/nf-core/picard/filtersamreads/main.nf index 847bee57dec..9fe3e04b0b5 100644 --- a/tests/modules/nf-core/picard/filtersamreads/main.nf +++ b/tests/modules/nf-core/picard/filtersamreads/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' -include { PICARD_FILTERSAMREADS } from '../../../../modules/picard/filtersamreads/main.nf' +include { PICARD_SORTSAM } from '../../../../modules/nf-core/picard/sortsam/main.nf' +include { PICARD_FILTERSAMREADS } from '../../../../modules/nf-core/picard/filtersamreads/main.nf' workflow test_picard_filtersamreads { diff --git a/tests/modules/nf-core/picard/fixmateinformation/main.nf b/tests/modules/nf-core/picard/fixmateinformation/main.nf index 46b4248b91f..0cdccd14e0e 100644 --- a/tests/modules/nf-core/picard/fixmateinformation/main.nf +++ b/tests/modules/nf-core/picard/fixmateinformation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_FIXMATEINFORMATION } from '../../../../modules/picard/fixmateinformation/main.nf' +include { PICARD_FIXMATEINFORMATION } from '../../../../modules/nf-core/picard/fixmateinformation/main.nf' workflow test_picard_fixmateinformation { diff --git a/tests/modules/nf-core/picard/liftovervcf/main.nf b/tests/modules/nf-core/picard/liftovervcf/main.nf index 08181a8a723..20cff729b7e 100644 --- a/tests/modules/nf-core/picard/liftovervcf/main.nf +++ b/tests/modules/nf-core/picard/liftovervcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_LIFTOVERVCF } from '../../../../modules/picard/liftovervcf/main.nf' +include { PICARD_LIFTOVERVCF } from '../../../../modules/nf-core/picard/liftovervcf/main.nf' workflow test_picard_liftovervcf { diff --git a/tests/modules/nf-core/picard/markduplicates/main.nf b/tests/modules/nf-core/picard/markduplicates/main.nf index 12f3ac26afc..33ac5f55a35 100644 --- a/tests/modules/nf-core/picard/markduplicates/main.nf +++ b/tests/modules/nf-core/picard/markduplicates/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' -include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' +include { PICARD_MARKDUPLICATES } from '../../../../modules/nf-core/picard/markduplicates/main.nf' +include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/nf-core/picard/markduplicates/main.nf' workflow test_picard_markduplicates_sorted_bam { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/picard/mergesamfiles/main.nf b/tests/modules/nf-core/picard/mergesamfiles/main.nf index 51c070b645c..a02e0656ede 100644 --- a/tests/modules/nf-core/picard/mergesamfiles/main.nf +++ b/tests/modules/nf-core/picard/mergesamfiles/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_MERGESAMFILES } from '../../../../modules/picard/mergesamfiles/main.nf' +include { PICARD_MERGESAMFILES } from '../../../../modules/nf-core/picard/mergesamfiles/main.nf' workflow test_picard_mergesamfiles { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf index 1516682cf27..70f8a267419 100644 --- a/tests/modules/nf-core/picard/sortsam/main.nf +++ b/tests/modules/nf-core/picard/sortsam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' +include { PICARD_SORTSAM } from '../../../../modules/nf-core/picard/sortsam/main.nf' workflow test_picard_sortsam { diff --git a/tests/modules/nf-core/picard/sortvcf/main.nf b/tests/modules/nf-core/picard/sortvcf/main.nf index a88c69fc768..0b56089e695 100644 --- a/tests/modules/nf-core/picard/sortvcf/main.nf +++ b/tests/modules/nf-core/picard/sortvcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTVCF } from '../../../../modules/picard/sortvcf/main.nf' +include { PICARD_SORTVCF } from '../../../../modules/nf-core/picard/sortvcf/main.nf' workflow test_picard_sortvcf { diff --git a/tests/modules/nf-core/pints/caller/main.nf b/tests/modules/nf-core/pints/caller/main.nf index 6dd7938dda7..0f69cda4191 100644 --- a/tests/modules/nf-core/pints/caller/main.nf +++ b/tests/modules/nf-core/pints/caller/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PINTS_CALLER } from '../../../../modules/pints/caller/main.nf' +include { PINTS_CALLER } from '../../../../modules/nf-core/pints/caller/main.nf' workflow test_pints_caller { diff --git a/tests/modules/nf-core/pirate/main.nf b/tests/modules/nf-core/pirate/main.nf index 45c60713af4..11c60f43295 100644 --- a/tests/modules/nf-core/pirate/main.nf +++ b/tests/modules/nf-core/pirate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PIRATE } from '../../../modules/pirate/main.nf' +include { PIRATE } from '../../../modules/nf-core/pirate/main.nf' workflow test_pirate { diff --git a/tests/modules/nf-core/plasmidfinder/main.nf b/tests/modules/nf-core/plasmidfinder/main.nf index 518d135e940..08dd396e1ee 100644 --- a/tests/modules/nf-core/plasmidfinder/main.nf +++ b/tests/modules/nf-core/plasmidfinder/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLASMIDFINDER } from '../../../modules/plasmidfinder/main.nf' +include { PLASMIDFINDER } from '../../../modules/nf-core/plasmidfinder/main.nf' workflow test_plasmidfinder { diff --git a/tests/modules/nf-core/plasmidid/main.nf b/tests/modules/nf-core/plasmidid/main.nf index 52d25a91014..e47230828f8 100644 --- a/tests/modules/nf-core/plasmidid/main.nf +++ b/tests/modules/nf-core/plasmidid/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLASMIDID } from '../../../modules/plasmidid/main.nf' +include { PLASMIDID } from '../../../modules/nf-core/plasmidid/main.nf' workflow test_plasmidid { diff --git a/tests/modules/nf-core/plink/extract/main.nf b/tests/modules/nf-core/plink/extract/main.nf index 6beb0469284..806959b8d1b 100644 --- a/tests/modules/nf-core/plink/extract/main.nf +++ b/tests/modules/nf-core/plink/extract/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' -include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf' +include { PLINK_VCF } from '../../../../modules/nf-core/plink/vcf/main.nf' +include { PLINK_EXTRACT } from '../../../../modules/nf-core/plink/extract/main.nf' workflow test_plink_extract { diff --git a/tests/modules/nf-core/plink/vcf/main.nf b/tests/modules/nf-core/plink/vcf/main.nf index 4dac8978247..1cac7969f86 100644 --- a/tests/modules/nf-core/plink/vcf/main.nf +++ b/tests/modules/nf-core/plink/vcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' +include { PLINK_VCF } from '../../../../modules/nf-core/plink/vcf/main.nf' workflow test_plink_vcf { diff --git a/tests/modules/nf-core/plink2/extract/main.nf b/tests/modules/nf-core/plink2/extract/main.nf index a72e153c9cc..7f00ef29fd8 100644 --- a/tests/modules/nf-core/plink2/extract/main.nf +++ b/tests/modules/nf-core/plink2/extract/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf' -include { PLINK2_EXTRACT } from '../../../../modules/plink2/extract/main.nf' +include { PLINK2_VCF } from '../../../../modules/nf-core/plink2/vcf/main.nf' +include { PLINK2_EXTRACT } from '../../../../modules/nf-core/plink2/extract/main.nf' workflow test_plink2_extract { diff --git a/tests/modules/nf-core/plink2/score/main.nf b/tests/modules/nf-core/plink2/score/main.nf index 6a09e8294b9..f9a2692209d 100644 --- a/tests/modules/nf-core/plink2/score/main.nf +++ b/tests/modules/nf-core/plink2/score/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf' -include { PLINK2_SCORE } from '../../../../modules/plink2/score/main.nf' +include { PLINK2_VCF } from '../../../../modules/nf-core/plink2/vcf/main.nf' +include { PLINK2_SCORE } from '../../../../modules/nf-core/plink2/score/main.nf' workflow test_plink2_score { input = [ diff --git a/tests/modules/nf-core/plink2/vcf/main.nf b/tests/modules/nf-core/plink2/vcf/main.nf index 08d7dc611ae..e417922b3b6 100644 --- a/tests/modules/nf-core/plink2/vcf/main.nf +++ b/tests/modules/nf-core/plink2/vcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf' +include { PLINK2_VCF } from '../../../../modules/nf-core/plink2/vcf/main.nf' workflow test_plink2_vcf { diff --git a/tests/modules/nf-core/pmdtools/filter/main.nf b/tests/modules/nf-core/pmdtools/filter/main.nf index f1b2b4d3fb1..6d9973e825a 100644 --- a/tests/modules/nf-core/pmdtools/filter/main.nf +++ b/tests/modules/nf-core/pmdtools/filter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PMDTOOLS_FILTER } from '../../../../modules/pmdtools/filter/main.nf' +include { PMDTOOLS_FILTER } from '../../../../modules/nf-core/pmdtools/filter/main.nf' workflow test_pmdtools_filter { diff --git a/tests/modules/nf-core/porechop/main.nf b/tests/modules/nf-core/porechop/main.nf index f20b7a6efd5..fb6ae0e7dd2 100644 --- a/tests/modules/nf-core/porechop/main.nf +++ b/tests/modules/nf-core/porechop/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PORECHOP } from '../../../modules/porechop/main.nf' +include { PORECHOP } from '../../../modules/nf-core/porechop/main.nf' workflow test_porechop { diff --git a/tests/modules/nf-core/preseq/ccurve/main.nf b/tests/modules/nf-core/preseq/ccurve/main.nf index 59149563c4f..1c03a1eb87e 100644 --- a/tests/modules/nf-core/preseq/ccurve/main.nf +++ b/tests/modules/nf-core/preseq/ccurve/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRESEQ_CCURVE } from '../../../../modules/preseq/ccurve/main.nf' +include { PRESEQ_CCURVE } from '../../../../modules/nf-core/preseq/ccurve/main.nf' workflow test_preseq_ccurve_single_end { diff --git a/tests/modules/nf-core/preseq/lcextrap/main.nf b/tests/modules/nf-core/preseq/lcextrap/main.nf index 4bbbd146c24..24028337dcf 100644 --- a/tests/modules/nf-core/preseq/lcextrap/main.nf +++ b/tests/modules/nf-core/preseq/lcextrap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRESEQ_LCEXTRAP } from '../../../../modules/preseq/lcextrap/main.nf' +include { PRESEQ_LCEXTRAP } from '../../../../modules/nf-core/preseq/lcextrap/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/prinseqplusplus/main.nf b/tests/modules/nf-core/prinseqplusplus/main.nf index d6ee3be9e59..2b162110967 100644 --- a/tests/modules/nf-core/prinseqplusplus/main.nf +++ b/tests/modules/nf-core/prinseqplusplus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRINSEQPLUSPLUS } from '../../../modules/prinseqplusplus/main.nf' +include { PRINSEQPLUSPLUS } from '../../../modules/nf-core/prinseqplusplus/main.nf' workflow test_prinseqplusplus_single_end { diff --git a/tests/modules/nf-core/prodigal/main.nf b/tests/modules/nf-core/prodigal/main.nf index 6e2820151a3..fcbff592a39 100644 --- a/tests/modules/nf-core/prodigal/main.nf +++ b/tests/modules/nf-core/prodigal/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRODIGAL } from '../../../modules/prodigal/main.nf' +include { PRODIGAL } from '../../../modules/nf-core/prodigal/main.nf' workflow test_prodigal { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/prokka/main.nf b/tests/modules/nf-core/prokka/main.nf index 97e94ca8beb..8b2380da35f 100644 --- a/tests/modules/nf-core/prokka/main.nf +++ b/tests/modules/nf-core/prokka/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PROKKA } from '../../../modules/prokka/main.nf' +include { PROKKA } from '../../../modules/nf-core/prokka/main.nf' workflow test_prokka { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/pycoqc/main.nf b/tests/modules/nf-core/pycoqc/main.nf index c8a8ee2c15f..2e2ddd3c4b0 100644 --- a/tests/modules/nf-core/pycoqc/main.nf +++ b/tests/modules/nf-core/pycoqc/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PYCOQC } from '../../../modules/pycoqc/main.nf' +include { PYCOQC } from '../../../modules/nf-core/pycoqc/main.nf' workflow test_pycoqc { diff --git a/tests/modules/nf-core/pydamage/analyze/main.nf b/tests/modules/nf-core/pydamage/analyze/main.nf index 920a4201953..ea67412dc65 100644 --- a/tests/modules/nf-core/pydamage/analyze/main.nf +++ b/tests/modules/nf-core/pydamage/analyze/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf' +include { PYDAMAGE_ANALYZE } from '../../../../modules/nf-core/pydamage/analyze/main.nf' workflow test_pydamage { diff --git a/tests/modules/nf-core/pydamage/filter/main.nf b/tests/modules/nf-core/pydamage/filter/main.nf index dac03e7879a..dd0d2588447 100644 --- a/tests/modules/nf-core/pydamage/filter/main.nf +++ b/tests/modules/nf-core/pydamage/filter/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf' -include { PYDAMAGE_FILTER } from '../../../../modules/pydamage/filter/main.nf' +include { PYDAMAGE_ANALYZE } from '../../../../modules/nf-core/pydamage/analyze/main.nf' +include { PYDAMAGE_FILTER } from '../../../../modules/nf-core/pydamage/filter/main.nf' workflow test_pydamage { diff --git a/tests/modules/nf-core/qcat/main.nf b/tests/modules/nf-core/qcat/main.nf index 8a5cdd6d8fd..196e54e6674 100644 --- a/tests/modules/nf-core/qcat/main.nf +++ b/tests/modules/nf-core/qcat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QCAT } from '../../../modules/qcat/main.nf' +include { QCAT } from '../../../modules/nf-core/qcat/main.nf' workflow test_qcat { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/qualimap/bamqc/main.nf b/tests/modules/nf-core/qualimap/bamqc/main.nf index 623634e4737..bfd61ff38ae 100644 --- a/tests/modules/nf-core/qualimap/bamqc/main.nf +++ b/tests/modules/nf-core/qualimap/bamqc/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QUALIMAP_BAMQC } from '../../../../modules/qualimap/bamqc/main.nf' +include { QUALIMAP_BAMQC } from '../../../../modules/nf-core/qualimap/bamqc/main.nf' workflow test_qualimap_bamqc { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/qualimap/bamqccram/main.nf b/tests/modules/nf-core/qualimap/bamqccram/main.nf index e4d8433e59b..b1b7c0ea5a6 100644 --- a/tests/modules/nf-core/qualimap/bamqccram/main.nf +++ b/tests/modules/nf-core/qualimap/bamqccram/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QUALIMAP_BAMQCCRAM } from '../../../../modules/qualimap/bamqccram/main.nf' +include { QUALIMAP_BAMQCCRAM } from '../../../../modules/nf-core/qualimap/bamqccram/main.nf' workflow test_qualimap_bamqc { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/quast/main.nf b/tests/modules/nf-core/quast/main.nf index c879a8a97e1..fc99bd494f9 100644 --- a/tests/modules/nf-core/quast/main.nf +++ b/tests/modules/nf-core/quast/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QUAST } from '../../../modules/quast/main.nf' +include { QUAST } from '../../../modules/nf-core/quast/main.nf' workflow test_quast_ref { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/racon/main.nf b/tests/modules/nf-core/racon/main.nf index 507d8d8d95d..37812aacca3 100644 --- a/tests/modules/nf-core/racon/main.nf +++ b/tests/modules/nf-core/racon/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RACON } from '../../../modules/racon/main.nf' +include { RACON } from '../../../modules/nf-core/racon/main.nf' workflow test_racon { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/rapidnj/main.nf b/tests/modules/nf-core/rapidnj/main.nf index 66d19c3c74e..b3209a67df5 100644 --- a/tests/modules/nf-core/rapidnj/main.nf +++ b/tests/modules/nf-core/rapidnj/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RAPIDNJ } from '../../../modules/rapidnj/main.nf' +include { RAPIDNJ } from '../../../modules/nf-core/rapidnj/main.nf' workflow test_rapidnj { diff --git a/tests/modules/nf-core/rasusa/main.nf b/tests/modules/nf-core/rasusa/main.nf index 8a11627c986..48120746e11 100644 --- a/tests/modules/nf-core/rasusa/main.nf +++ b/tests/modules/nf-core/rasusa/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RASUSA } from '../../../modules/rasusa/main.nf' +include { RASUSA } from '../../../modules/nf-core/rasusa/main.nf' workflow test_rasusa { input = [ [ id:'test', single_end:false], // meta map diff --git a/tests/modules/nf-core/raven/main.nf b/tests/modules/nf-core/raven/main.nf index 01b0451999b..a126158d8ec 100644 --- a/tests/modules/nf-core/raven/main.nf +++ b/tests/modules/nf-core/raven/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RAVEN } from '../../../modules/raven/main.nf' +include { RAVEN } from '../../../modules/nf-core/raven/main.nf' workflow test_raven { diff --git a/tests/modules/nf-core/raxmlng/main.nf b/tests/modules/nf-core/raxmlng/main.nf index 5fad6953b56..8450af59865 100644 --- a/tests/modules/nf-core/raxmlng/main.nf +++ b/tests/modules/nf-core/raxmlng/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../modules/raxmlng/main.nf' -include { RAXMLNG as RAXMLNG_BOOTSTRAP } from '../../../modules/raxmlng/main.nf' +include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../modules/nf-core/raxmlng/main.nf' +include { RAXMLNG as RAXMLNG_BOOTSTRAP } from '../../../modules/nf-core/raxmlng/main.nf' // // Test without bootstrapping diff --git a/tests/modules/nf-core/rgi/main/main.nf b/tests/modules/nf-core/rgi/main/main.nf index 9182a1548d5..b30c83403e9 100644 --- a/tests/modules/nf-core/rgi/main/main.nf +++ b/tests/modules/nf-core/rgi/main/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf' +include { RGI_MAIN } from '../../../../modules/nf-core/rgi/main/main.nf' workflow test_rgi_main { diff --git a/tests/modules/nf-core/rhocall/annotate/main.nf b/tests/modules/nf-core/rhocall/annotate/main.nf index 9cca1520f3c..fcc156d3997 100644 --- a/tests/modules/nf-core/rhocall/annotate/main.nf +++ b/tests/modules/nf-core/rhocall/annotate/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RHOCALL_ANNOTATE } from '../../../../modules/rhocall/annotate/main.nf' -include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf' +include { RHOCALL_ANNOTATE } from '../../../../modules/nf-core/rhocall/annotate/main.nf' +include { BCFTOOLS_ROH } from '../../../../modules/nf-core/bcftools/roh/main.nf' workflow test_rhocall_annotate { diff --git a/tests/modules/nf-core/rmarkdownnotebook/main.nf b/tests/modules/nf-core/rmarkdownnotebook/main.nf index fdb7d3b9941..4b1777a2e21 100644 --- a/tests/modules/nf-core/rmarkdownnotebook/main.nf +++ b/tests/modules/nf-core/rmarkdownnotebook/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RMARKDOWNNOTEBOOK } from '../../../modules/rmarkdownnotebook/main.nf' -include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/rmarkdownnotebook/main.nf' +include { RMARKDOWNNOTEBOOK } from '../../../modules/nf-core/rmarkdownnotebook/main.nf' +include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/nf-core/rmarkdownnotebook/main.nf' workflow test_rmarkdown { diff --git a/tests/modules/nf-core/roary/main.nf b/tests/modules/nf-core/roary/main.nf index 3fae516ce8a..07d896fbada 100644 --- a/tests/modules/nf-core/roary/main.nf +++ b/tests/modules/nf-core/roary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ROARY } from '../../../modules/roary/main.nf' +include { ROARY } from '../../../modules/nf-core/roary/main.nf' workflow test_roary { diff --git a/tests/modules/nf-core/rsem/calculateexpression/main.nf b/tests/modules/nf-core/rsem/calculateexpression/main.nf index 9d6d3c5cfa1..57d9249ce86 100644 --- a/tests/modules/nf-core/rsem/calculateexpression/main.nf +++ b/tests/modules/nf-core/rsem/calculateexpression/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' -include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' +include { RSEM_PREPAREREFERENCE } from '../../../../modules/nf-core/rsem/preparereference/main.nf' +include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/nf-core/rsem/calculateexpression/main.nf' workflow test_rsem_calculateexpression { diff --git a/tests/modules/nf-core/rsem/preparereference/main.nf b/tests/modules/nf-core/rsem/preparereference/main.nf index 8062737de57..276fa74a2f5 100644 --- a/tests/modules/nf-core/rsem/preparereference/main.nf +++ b/tests/modules/nf-core/rsem/preparereference/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' +include { RSEM_PREPAREREFERENCE } from '../../../../modules/nf-core/rsem/preparereference/main.nf' workflow test_rsem_preparereference { diff --git a/tests/modules/nf-core/rseqc/bamstat/main.nf b/tests/modules/nf-core/rseqc/bamstat/main.nf index 4c53a1af0ad..d2c4c779014 100644 --- a/tests/modules/nf-core/rseqc/bamstat/main.nf +++ b/tests/modules/nf-core/rseqc/bamstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_BAMSTAT } from '../../../../modules/rseqc/bamstat/main.nf' +include { RSEQC_BAMSTAT } from '../../../../modules/nf-core/rseqc/bamstat/main.nf' workflow test_rseqc_bamstat { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/rseqc/inferexperiment/main.nf b/tests/modules/nf-core/rseqc/inferexperiment/main.nf index 6337063de75..043fd01973f 100644 --- a/tests/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/tests/modules/nf-core/rseqc/inferexperiment/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_INFEREXPERIMENT } from '../../../../modules/rseqc/inferexperiment/main.nf' +include { RSEQC_INFEREXPERIMENT } from '../../../../modules/nf-core/rseqc/inferexperiment/main.nf' workflow test_rseqc_inferexperiment { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/rseqc/innerdistance/main.nf b/tests/modules/nf-core/rseqc/innerdistance/main.nf index 8cc0ec3eebc..b44db9e49a7 100644 --- a/tests/modules/nf-core/rseqc/innerdistance/main.nf +++ b/tests/modules/nf-core/rseqc/innerdistance/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_INNERDISTANCE } from '../../../../modules/rseqc/innerdistance/main.nf' +include { RSEQC_INNERDISTANCE } from '../../../../modules/nf-core/rseqc/innerdistance/main.nf' workflow test_rseqc_innerdistance { input = [ [ id:'test', single_end: false ], // meta map diff --git a/tests/modules/nf-core/rseqc/junctionannotation/main.nf b/tests/modules/nf-core/rseqc/junctionannotation/main.nf index 303dcd854df..1dc7983063f 100644 --- a/tests/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/tests/modules/nf-core/rseqc/junctionannotation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_JUNCTIONANNOTATION } from '../../../../modules/rseqc/junctionannotation/main.nf' +include { RSEQC_JUNCTIONANNOTATION } from '../../../../modules/nf-core/rseqc/junctionannotation/main.nf' workflow test_rseqc_junctionannotation { input = [ diff --git a/tests/modules/nf-core/rseqc/junctionsaturation/main.nf b/tests/modules/nf-core/rseqc/junctionsaturation/main.nf index eefbb492063..dd3a8fa1706 100644 --- a/tests/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/tests/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_JUNCTIONSATURATION } from '../../../../modules/rseqc/junctionsaturation/main.nf' +include { RSEQC_JUNCTIONSATURATION } from '../../../../modules/nf-core/rseqc/junctionsaturation/main.nf' workflow test_rseqc_junctionsaturation { input = [ diff --git a/tests/modules/nf-core/rseqc/readdistribution/main.nf b/tests/modules/nf-core/rseqc/readdistribution/main.nf index 180367f2600..130a2ac1d5b 100644 --- a/tests/modules/nf-core/rseqc/readdistribution/main.nf +++ b/tests/modules/nf-core/rseqc/readdistribution/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_READDISTRIBUTION } from '../../../../modules/rseqc/readdistribution/main.nf' +include { RSEQC_READDISTRIBUTION } from '../../../../modules/nf-core/rseqc/readdistribution/main.nf' workflow test_rseqc_readdistribution { input = [ [ id:'test', single_end: false ], // meta map diff --git a/tests/modules/nf-core/rseqc/readduplication/main.nf b/tests/modules/nf-core/rseqc/readduplication/main.nf index bcccde5d504..07236b53626 100644 --- a/tests/modules/nf-core/rseqc/readduplication/main.nf +++ b/tests/modules/nf-core/rseqc/readduplication/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_READDUPLICATION } from '../../../../modules/rseqc/readduplication/main.nf' +include { RSEQC_READDUPLICATION } from '../../../../modules/nf-core/rseqc/readduplication/main.nf' workflow test_rseqc_readduplication { input = [ [ id:'test', single_end: false ], // meta map diff --git a/tests/modules/nf-core/rseqc/tin/main.nf b/tests/modules/nf-core/rseqc/tin/main.nf index 677e116535d..adb294cfcdb 100644 --- a/tests/modules/nf-core/rseqc/tin/main.nf +++ b/tests/modules/nf-core/rseqc/tin/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_TIN } from '../../../../modules/rseqc/tin/main.nf' +include { RSEQC_TIN } from '../../../../modules/nf-core/rseqc/tin/main.nf' workflow test_rseqc_tin { diff --git a/tests/modules/nf-core/rtgtools/pedfilter/main.nf b/tests/modules/nf-core/rtgtools/pedfilter/main.nf index a8361e6dee1..f667e8f55d9 100644 --- a/tests/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/tests/modules/nf-core/rtgtools/pedfilter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RTGTOOLS_PEDFILTER } from '../../../../modules/rtgtools/pedfilter/main.nf' +include { RTGTOOLS_PEDFILTER } from '../../../../modules/nf-core/rtgtools/pedfilter/main.nf' workflow test_rtgtools_pedfilter { diff --git a/tests/modules/nf-core/rtgtools/vcfeval/main.nf b/tests/modules/nf-core/rtgtools/vcfeval/main.nf index 9a1c3c71faf..8c65581bcd9 100644 --- a/tests/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/tests/modules/nf-core/rtgtools/vcfeval/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf' -include { UNTAR } from '../../../modules/untar/main.nf' +include { RTGTOOLS_VCFEVAL } from '../../../../modules/nf-core/rtgtools/vcfeval/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' workflow test_rtgtools_vcfeval { diff --git a/tests/modules/nf-core/salmon/index/main.nf b/tests/modules/nf-core/salmon/index/main.nf index 680b4c6e5a2..55525b4eeee 100644 --- a/tests/modules/nf-core/salmon/index/main.nf +++ b/tests/modules/nf-core/salmon/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' +include { SALMON_INDEX } from '../../../../modules/nf-core/salmon/index/main.nf' workflow test_salmon_index { genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/salmon/quant/main.nf b/tests/modules/nf-core/salmon/quant/main.nf index a970f6c5177..8cf2b1b00e3 100644 --- a/tests/modules/nf-core/salmon/quant/main.nf +++ b/tests/modules/nf-core/salmon/quant/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' -include { SALMON_QUANT } from '../../../../modules/salmon/quant/main.nf' +include { SALMON_INDEX } from '../../../../modules/nf-core/salmon/index/main.nf' +include { SALMON_QUANT } from '../../../../modules/nf-core/salmon/quant/main.nf' workflow test_salmon_quant_single_end { diff --git a/tests/modules/nf-core/samblaster/main.nf b/tests/modules/nf-core/samblaster/main.nf index 5831ecfccd6..17e769f5419 100644 --- a/tests/modules/nf-core/samblaster/main.nf +++ b/tests/modules/nf-core/samblaster/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMBLASTER } from '../../../modules/samblaster/main.nf' +include { SAMBLASTER } from '../../../modules/nf-core/samblaster/main.nf' workflow test_samblaster { diff --git a/tests/modules/nf-core/samtools/ampliconclip/main.nf b/tests/modules/nf-core/samtools/ampliconclip/main.nf index eae70b06fb8..2b2646bc3ca 100644 --- a/tests/modules/nf-core/samtools/ampliconclip/main.nf +++ b/tests/modules/nf-core/samtools/ampliconclip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf' +include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/nf-core/samtools/ampliconclip/main.nf' workflow test_samtools_ampliconclip_no_stats_no_rejects { diff --git a/tests/modules/nf-core/samtools/bam2fq/main.nf b/tests/modules/nf-core/samtools/bam2fq/main.nf index 928bfe081c4..70c8fe864bf 100644 --- a/tests/modules/nf-core/samtools/bam2fq/main.nf +++ b/tests/modules/nf-core/samtools/bam2fq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_BAM2FQ } from '../../../../modules/samtools/bam2fq/main.nf' +include { SAMTOOLS_BAM2FQ } from '../../../../modules/nf-core/samtools/bam2fq/main.nf' workflow test_samtools_bam2fq_nosplit { diff --git a/tests/modules/nf-core/samtools/collate/main.nf b/tests/modules/nf-core/samtools/collate/main.nf index 5fec4913ab1..34b62eef42e 100644 --- a/tests/modules/nf-core/samtools/collate/main.nf +++ b/tests/modules/nf-core/samtools/collate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf' +include { SAMTOOLS_COLLATE } from '../../../../modules/nf-core/samtools/collate/main.nf' workflow test_samtools_collate { diff --git a/tests/modules/nf-core/samtools/collatefastq/main.nf b/tests/modules/nf-core/samtools/collatefastq/main.nf index 928742acc18..2c629750351 100644 --- a/tests/modules/nf-core/samtools/collatefastq/main.nf +++ b/tests/modules/nf-core/samtools/collatefastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COLLATEFASTQ } from '../../../../modules/samtools/collatefastq/main.nf' +include { SAMTOOLS_COLLATEFASTQ } from '../../../../modules/nf-core/samtools/collatefastq/main.nf' workflow test_samtools_collatefastq { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/convert/main.nf b/tests/modules/nf-core/samtools/convert/main.nf index 01bdfe7f531..cdde49aa94a 100644 --- a/tests/modules/nf-core/samtools/convert/main.nf +++ b/tests/modules/nf-core/samtools/convert/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf' -include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf' +include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/nf-core/samtools/convert/main.nf' +include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/nf-core/samtools/convert/main.nf' workflow test_samtools_convert_bamtocram { diff --git a/tests/modules/nf-core/samtools/depth/main.nf b/tests/modules/nf-core/samtools/depth/main.nf index c6d2dc0e7b9..4d88ac588ce 100644 --- a/tests/modules/nf-core/samtools/depth/main.nf +++ b/tests/modules/nf-core/samtools/depth/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_DEPTH } from '../../../../modules/samtools/depth/main.nf' +include { SAMTOOLS_DEPTH } from '../../../../modules/nf-core/samtools/depth/main.nf' workflow test_samtools_depth { diff --git a/tests/modules/nf-core/samtools/dict/main.nf b/tests/modules/nf-core/samtools/dict/main.nf index f24a83829aa..b05fde55c57 100644 --- a/tests/modules/nf-core/samtools/dict/main.nf +++ b/tests/modules/nf-core/samtools/dict/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_DICT } from '../../../../modules/samtools/dict/main.nf' +include { SAMTOOLS_DICT } from '../../../../modules/nf-core/samtools/dict/main.nf' workflow test_samtools_dict { diff --git a/tests/modules/nf-core/samtools/faidx/main.nf b/tests/modules/nf-core/samtools/faidx/main.nf index ea8a2947d15..0f55475c025 100644 --- a/tests/modules/nf-core/samtools/faidx/main.nf +++ b/tests/modules/nf-core/samtools/faidx/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FAIDX } from '../../../../modules/samtools/faidx/main.nf' +include { SAMTOOLS_FAIDX } from '../../../../modules/nf-core/samtools/faidx/main.nf' workflow test_samtools_faidx { diff --git a/tests/modules/nf-core/samtools/fasta/main.nf b/tests/modules/nf-core/samtools/fasta/main.nf index c0ef91f4fd8..83b68728653 100644 --- a/tests/modules/nf-core/samtools/fasta/main.nf +++ b/tests/modules/nf-core/samtools/fasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FASTA } from '../../../../modules/samtools/fasta/main.nf' +include { SAMTOOLS_FASTA } from '../../../../modules/nf-core/samtools/fasta/main.nf' workflow test_samtools_fasta { diff --git a/tests/modules/nf-core/samtools/fastq/main.nf b/tests/modules/nf-core/samtools/fastq/main.nf index 6e7e323ca12..aa454e811a0 100644 --- a/tests/modules/nf-core/samtools/fastq/main.nf +++ b/tests/modules/nf-core/samtools/fastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FASTQ } from '../../../../modules/samtools/fastq/main.nf' +include { SAMTOOLS_FASTQ } from '../../../../modules/nf-core/samtools/fastq/main.nf' workflow test_samtools_fastq { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/fixmate/main.nf b/tests/modules/nf-core/samtools/fixmate/main.nf index cb7c136d25c..8da5be726b6 100644 --- a/tests/modules/nf-core/samtools/fixmate/main.nf +++ b/tests/modules/nf-core/samtools/fixmate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf' +include { SAMTOOLS_FIXMATE } from '../../../../modules/nf-core/samtools/fixmate/main.nf' workflow test_samtools_fixmate { diff --git a/tests/modules/nf-core/samtools/flagstat/main.nf b/tests/modules/nf-core/samtools/flagstat/main.nf index a0e86422276..bb30f518be4 100644 --- a/tests/modules/nf-core/samtools/flagstat/main.nf +++ b/tests/modules/nf-core/samtools/flagstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FLAGSTAT } from '../../../../modules/samtools/flagstat/main.nf' +include { SAMTOOLS_FLAGSTAT } from '../../../../modules/nf-core/samtools/flagstat/main.nf' workflow test_samtools_flagstat { input = [ diff --git a/tests/modules/nf-core/samtools/getrg/main.nf b/tests/modules/nf-core/samtools/getrg/main.nf index 3e92149e270..3ce9f80c9c2 100644 --- a/tests/modules/nf-core/samtools/getrg/main.nf +++ b/tests/modules/nf-core/samtools/getrg/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_GETRG } from '../../../../modules/samtools/getrg/main.nf' +include { SAMTOOLS_GETRG } from '../../../../modules/nf-core/samtools/getrg/main.nf' workflow test_samtools_getrg { diff --git a/tests/modules/nf-core/samtools/idxstats/main.nf b/tests/modules/nf-core/samtools/idxstats/main.nf index f3de76a0d82..83b0607e30a 100644 --- a/tests/modules/nf-core/samtools/idxstats/main.nf +++ b/tests/modules/nf-core/samtools/idxstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_IDXSTATS } from '../../../../modules/samtools/idxstats/main.nf' +include { SAMTOOLS_IDXSTATS } from '../../../../modules/nf-core/samtools/idxstats/main.nf' workflow test_samtools_idxstats { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/index/main.nf b/tests/modules/nf-core/samtools/index/main.nf index 3592a99a5ec..ff952b5a36b 100644 --- a/tests/modules/nf-core/samtools/index/main.nf +++ b/tests/modules/nf-core/samtools/index/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/samtools/index/main.nf' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/samtools/index/main.nf' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/samtools/index/main.nf' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/nf-core/samtools/index/main.nf' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/nf-core/samtools/index/main.nf' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/nf-core/samtools/index/main.nf' workflow test_samtools_index_bai { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/markdup/main.nf b/tests/modules/nf-core/samtools/markdup/main.nf index 0628e3d75fe..f96bfc55442 100644 --- a/tests/modules/nf-core/samtools/markdup/main.nf +++ b/tests/modules/nf-core/samtools/markdup/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf' -include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf' -include { SAMTOOLS_SORT } from '../../../../modules/samtools/sort/main.nf' -include { SAMTOOLS_MARKDUP } from '../../../../modules/samtools/markdup/main.nf' +include { SAMTOOLS_COLLATE } from '../../../../modules/nf-core/samtools/collate/main.nf' +include { SAMTOOLS_FIXMATE } from '../../../../modules/nf-core/samtools/fixmate/main.nf' +include { SAMTOOLS_SORT } from '../../../../modules/nf-core/samtools/sort/main.nf' +include { SAMTOOLS_MARKDUP } from '../../../../modules/nf-core/samtools/markdup/main.nf' workflow test_samtools_markdup { diff --git a/tests/modules/nf-core/samtools/merge/main.nf b/tests/modules/nf-core/samtools/merge/main.nf index 0d01eb7203c..3e41ffc7769 100644 --- a/tests/modules/nf-core/samtools/merge/main.nf +++ b/tests/modules/nf-core/samtools/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf' +include { SAMTOOLS_MERGE } from '../../../../modules/nf-core/samtools/merge/main.nf' workflow test_samtools_merge { input = [ [ id: 'test' ], // meta map diff --git a/tests/modules/nf-core/samtools/mpileup/main.nf b/tests/modules/nf-core/samtools/mpileup/main.nf index f7fd4b43e06..4ee131c29bf 100644 --- a/tests/modules/nf-core/samtools/mpileup/main.nf +++ b/tests/modules/nf-core/samtools/mpileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf' +include { SAMTOOLS_MPILEUP } from '../../../../modules/nf-core/samtools/mpileup/main.nf' workflow test_samtools_mpileup { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/sort/main.nf b/tests/modules/nf-core/samtools/sort/main.nf index 9853b3556ea..5b9d6890a46 100644 --- a/tests/modules/nf-core/samtools/sort/main.nf +++ b/tests/modules/nf-core/samtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_SORT } from '../../../../modules/samtools/sort/main.nf' +include { SAMTOOLS_SORT } from '../../../../modules/nf-core/samtools/sort/main.nf' workflow test_samtools_sort { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/stats/main.nf b/tests/modules/nf-core/samtools/stats/main.nf index d83cbf4a6f2..596ba1fcae8 100644 --- a/tests/modules/nf-core/samtools/stats/main.nf +++ b/tests/modules/nf-core/samtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_STATS } from '../../../../modules/samtools/stats/main.nf' +include { SAMTOOLS_STATS } from '../../../../modules/nf-core/samtools/stats/main.nf' workflow test_samtools_stats { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/view/main.nf b/tests/modules/nf-core/samtools/view/main.nf index e9db03ed09c..210a493adf1 100644 --- a/tests/modules/nf-core/samtools/view/main.nf +++ b/tests/modules/nf-core/samtools/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf' +include { SAMTOOLS_VIEW } from '../../../../modules/nf-core/samtools/view/main.nf' workflow test_samtools_view { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/scoary/main.nf b/tests/modules/nf-core/scoary/main.nf index 5f080b7d62d..59006b049e7 100644 --- a/tests/modules/nf-core/scoary/main.nf +++ b/tests/modules/nf-core/scoary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SCOARY } from '../../../modules/scoary/main.nf' +include { SCOARY } from '../../../modules/nf-core/scoary/main.nf' workflow test_scoary { diff --git a/tests/modules/nf-core/scramble/clusteranalysis/main.nf b/tests/modules/nf-core/scramble/clusteranalysis/main.nf index d31bac7201c..d9444c955d9 100644 --- a/tests/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/tests/modules/nf-core/scramble/clusteranalysis/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SCRAMBLE_CLUSTERANALYSIS } from '../../../../modules/scramble/clusteranalysis/main.nf' -include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/scramble/clusteridentifier/main.nf' +include { SCRAMBLE_CLUSTERANALYSIS } from '../../../../modules/nf-core/scramble/clusteranalysis/main.nf' +include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/nf-core/scramble/clusteridentifier/main.nf' workflow test_scramble_clusteranalysis { diff --git a/tests/modules/nf-core/scramble/clusteridentifier/main.nf b/tests/modules/nf-core/scramble/clusteridentifier/main.nf index 6aea7f535ab..1884a701881 100644 --- a/tests/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/tests/modules/nf-core/scramble/clusteridentifier/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/scramble/clusteridentifier/main.nf' +include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/nf-core/scramble/clusteridentifier/main.nf' workflow test_scramble_clusteridentifier_bam { diff --git a/tests/modules/nf-core/seacr/callpeak/main.nf b/tests/modules/nf-core/seacr/callpeak/main.nf index 230d3a4c15a..789e4f179bb 100644 --- a/tests/modules/nf-core/seacr/callpeak/main.nf +++ b/tests/modules/nf-core/seacr/callpeak/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' +include { SEACR_CALLPEAK } from '../../../../modules/nf-core/seacr/callpeak/main.nf' workflow test_seacr_callpeak { input = [ [ id:'test_1'], diff --git a/tests/modules/nf-core/seqkit/pair/main.nf b/tests/modules/nf-core/seqkit/pair/main.nf index 42bc9587780..b8b9070743d 100644 --- a/tests/modules/nf-core/seqkit/pair/main.nf +++ b/tests/modules/nf-core/seqkit/pair/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQKIT_PAIR } from '../../../../modules/seqkit/pair/main.nf' +include { SEQKIT_PAIR } from '../../../../modules/nf-core/seqkit/pair/main.nf' workflow test_seqkit_pair { diff --git a/tests/modules/nf-core/seqkit/replace/main.nf b/tests/modules/nf-core/seqkit/replace/main.nf index 5c4058e7a95..8cc2ce9ad9a 100644 --- a/tests/modules/nf-core/seqkit/replace/main.nf +++ b/tests/modules/nf-core/seqkit/replace/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SEQKIT_REPLACE } from '../../../../modules/seqkit/replace/main.nf' -include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../modules/seqkit/replace/main.nf' +include { SEQKIT_REPLACE } from '../../../../modules/nf-core/seqkit/replace/main.nf' +include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../modules/nf-core/seqkit/replace/main.nf' workflow test_seqkit_replace { diff --git a/tests/modules/nf-core/seqkit/split2/main.nf b/tests/modules/nf-core/seqkit/split2/main.nf index acb9d41bbb1..248e9f915cb 100644 --- a/tests/modules/nf-core/seqkit/split2/main.nf +++ b/tests/modules/nf-core/seqkit/split2/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../modules/seqkit/split2/main.nf' -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../modules/seqkit/split2/main.nf' -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../modules/seqkit/split2/main.nf' +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../modules/nf-core/seqkit/split2/main.nf' +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../modules/nf-core/seqkit/split2/main.nf' +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../modules/nf-core/seqkit/split2/main.nf' workflow test_seqkit_split2_single_end_length { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/seqkit/stats/main.nf b/tests/modules/nf-core/seqkit/stats/main.nf index 774421154d9..e516c834805 100644 --- a/tests/modules/nf-core/seqkit/stats/main.nf +++ b/tests/modules/nf-core/seqkit/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQKIT_STATS } from '../../../../modules/seqkit/stats/main.nf' +include { SEQKIT_STATS } from '../../../../modules/nf-core/seqkit/stats/main.nf' workflow test_seqkit_stats_single_end { diff --git a/tests/modules/nf-core/seqsero2/main.nf b/tests/modules/nf-core/seqsero2/main.nf index 9587bf9ffa5..b3ee1261bb7 100644 --- a/tests/modules/nf-core/seqsero2/main.nf +++ b/tests/modules/nf-core/seqsero2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQSERO2 } from '../../../modules/seqsero2/main.nf' +include { SEQSERO2 } from '../../../modules/nf-core/seqsero2/main.nf' workflow test_seqsero2 { diff --git a/tests/modules/nf-core/seqtk/mergepe/main.nf b/tests/modules/nf-core/seqtk/mergepe/main.nf index b8e12213ef7..9c980d5d976 100644 --- a/tests/modules/nf-core/seqtk/mergepe/main.nf +++ b/tests/modules/nf-core/seqtk/mergepe/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf' +include { SEQTK_MERGEPE } from '../../../../modules/nf-core/seqtk/mergepe/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/seqtk/rename/main.nf b/tests/modules/nf-core/seqtk/rename/main.nf index 1f81352d24b..ea48a880a33 100644 --- a/tests/modules/nf-core/seqtk/rename/main.nf +++ b/tests/modules/nf-core/seqtk/rename/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_RENAME } from '../../../../modules/seqtk/rename/main.nf' +include { SEQTK_RENAME } from '../../../../modules/nf-core/seqtk/rename/main.nf' workflow test_seqtk_rename { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seqtk/sample/main.nf b/tests/modules/nf-core/seqtk/sample/main.nf index 6899ef62fcc..e380a052b77 100644 --- a/tests/modules/nf-core/seqtk/sample/main.nf +++ b/tests/modules/nf-core/seqtk/sample/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_SAMPLE } from '../../../../modules/seqtk/sample/main.nf' +include { SEQTK_SAMPLE } from '../../../../modules/nf-core/seqtk/sample/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/seqtk/seq/main.nf b/tests/modules/nf-core/seqtk/seq/main.nf index 4351b8a961a..a30e1d3f1ac 100644 --- a/tests/modules/nf-core/seqtk/seq/main.nf +++ b/tests/modules/nf-core/seqtk/seq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_SEQ } from '../../../../modules/seqtk/seq/main.nf' +include { SEQTK_SEQ } from '../../../../modules/nf-core/seqtk/seq/main.nf' workflow test_seqtk_seq { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seqtk/subseq/main.nf b/tests/modules/nf-core/seqtk/subseq/main.nf index 608b7c2f069..28ad03af951 100644 --- a/tests/modules/nf-core/seqtk/subseq/main.nf +++ b/tests/modules/nf-core/seqtk/subseq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_SUBSEQ } from '../../../../modules/seqtk/subseq/main.nf' +include { SEQTK_SUBSEQ } from '../../../../modules/nf-core/seqtk/subseq/main.nf' workflow test_seqtk_subseq { diff --git a/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf b/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf index fcd4c7c721c..9da93c79af8 100755 --- a/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/sequenzautils/bam2seqz/main.nf' +include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/nf-core/sequenzautils/bam2seqz/main.nf' workflow test_sequenzautils_bam2seqz { diff --git a/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf b/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf index b25e037eb82..9e7da379e20 100644 --- a/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQUENZAUTILS_GCWIGGLE } from '../../../../modules/sequenzautils/gcwiggle/main.nf' +include { SEQUENZAUTILS_GCWIGGLE } from '../../../../modules/nf-core/sequenzautils/gcwiggle/main.nf' workflow test_sequenzautils_gcwiggle { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seqwish/induce/main.nf b/tests/modules/nf-core/seqwish/induce/main.nf index b83a904f2ff..c7e79c66198 100644 --- a/tests/modules/nf-core/seqwish/induce/main.nf +++ b/tests/modules/nf-core/seqwish/induce/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQWISH_INDUCE } from '../../../../modules/seqwish/induce/main.nf' +include { SEQWISH_INDUCE } from '../../../../modules/nf-core/seqwish/induce/main.nf' workflow test_seqwish_induce_transcriptome { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seroba/run/main.nf b/tests/modules/nf-core/seroba/run/main.nf index 62df1d3ff75..d848ddaa1b6 100644 --- a/tests/modules/nf-core/seroba/run/main.nf +++ b/tests/modules/nf-core/seroba/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEROBA_RUN } from '../../../../modules/seroba/run/main.nf' +include { SEROBA_RUN } from '../../../../modules/nf-core/seroba/run/main.nf' workflow test_seroba_run { diff --git a/tests/modules/nf-core/sexdeterrmine/main.nf b/tests/modules/nf-core/sexdeterrmine/main.nf index fc777905fec..6ad76a6e7fb 100644 --- a/tests/modules/nf-core/sexdeterrmine/main.nf +++ b/tests/modules/nf-core/sexdeterrmine/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_DEPTH } from '../../../modules/samtools/depth/main.nf' -include { SEXDETERRMINE } from '../../../modules/sexdeterrmine/main.nf' +include { SAMTOOLS_DEPTH } from '../../../modules/nf-core/samtools/depth/main.nf' +include { SEXDETERRMINE } from '../../../modules/nf-core/sexdeterrmine/main.nf' workflow test_sexdeterrmine { diff --git a/tests/modules/nf-core/shasta/main.nf b/tests/modules/nf-core/shasta/main.nf index 3838d1d4648..68bbce3d4b9 100644 --- a/tests/modules/nf-core/shasta/main.nf +++ b/tests/modules/nf-core/shasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SHASTA } from '../../../modules/shasta/main.nf' +include { SHASTA } from '../../../modules/nf-core/shasta/main.nf' workflow test_shasta { diff --git a/tests/modules/nf-core/shasum/main.nf b/tests/modules/nf-core/shasum/main.nf index 817ea6f08da..d3457d8c115 100644 --- a/tests/modules/nf-core/shasum/main.nf +++ b/tests/modules/nf-core/shasum/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SHASUM } from '../../../modules/shasum/main.nf' +include { SHASUM } from '../../../modules/nf-core/shasum/main.nf' workflow test_shasum { diff --git a/tests/modules/nf-core/shigatyper/main.nf b/tests/modules/nf-core/shigatyper/main.nf index eb4df084543..a234df007f2 100644 --- a/tests/modules/nf-core/shigatyper/main.nf +++ b/tests/modules/nf-core/shigatyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SHIGATYPER } from '../../../modules/shigatyper/main.nf' +include { SHIGATYPER } from '../../../modules/nf-core/shigatyper/main.nf' workflow test_shigatyper_pe { diff --git a/tests/modules/nf-core/shovill/main.nf b/tests/modules/nf-core/shovill/main.nf index 2416022f31a..6c48df62b35 100644 --- a/tests/modules/nf-core/shovill/main.nf +++ b/tests/modules/nf-core/shovill/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { SHOVILL } from '../../../modules/shovill/main.nf' -include { SHOVILL as SHOVILL_SKESA } from '../../../modules/shovill/main.nf' -include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/shovill/main.nf' -include { SHOVILL as SHOVILL_VELVET } from '../../../modules/shovill/main.nf' +include { SHOVILL } from '../../../modules/nf-core/shovill/main.nf' +include { SHOVILL as SHOVILL_SKESA } from '../../../modules/nf-core/shovill/main.nf' +include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/nf-core/shovill/main.nf' +include { SHOVILL as SHOVILL_VELVET } from '../../../modules/nf-core/shovill/main.nf' workflow test_shovill { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/sistr/main.nf b/tests/modules/nf-core/sistr/main.nf index 4bd8484470f..c25fe807855 100644 --- a/tests/modules/nf-core/sistr/main.nf +++ b/tests/modules/nf-core/sistr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SISTR } from '../../../modules/sistr/main.nf' +include { SISTR } from '../../../modules/nf-core/sistr/main.nf' workflow test_sistr { diff --git a/tests/modules/nf-core/slimfastq/main.nf b/tests/modules/nf-core/slimfastq/main.nf index 40d44285f42..a0ea9ab3e70 100644 --- a/tests/modules/nf-core/slimfastq/main.nf +++ b/tests/modules/nf-core/slimfastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SLIMFASTQ } from '../../../modules/slimfastq/main.nf' +include { SLIMFASTQ } from '../../../modules/nf-core/slimfastq/main.nf' workflow test_slimfastq_single_end { diff --git a/tests/modules/nf-core/snapaligner/align/main.nf b/tests/modules/nf-core/snapaligner/align/main.nf index 1a1c6d06968..b91302f32b3 100644 --- a/tests/modules/nf-core/snapaligner/align/main.nf +++ b/tests/modules/nf-core/snapaligner/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf' -include { SNAPALIGNER_ALIGN } from '../../../../modules/snapaligner/align/main.nf' +include { SNAPALIGNER_INDEX } from '../../../../modules/nf-core/snapaligner/index/main.nf' +include { SNAPALIGNER_ALIGN } from '../../../../modules/nf-core/snapaligner/align/main.nf' workflow test_snapaligner_single { diff --git a/tests/modules/nf-core/snapaligner/index/main.nf b/tests/modules/nf-core/snapaligner/index/main.nf index 4cebb876226..f43c40b3371 100644 --- a/tests/modules/nf-core/snapaligner/index/main.nf +++ b/tests/modules/nf-core/snapaligner/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf' +include { SNAPALIGNER_INDEX } from '../../../../modules/nf-core/snapaligner/index/main.nf' workflow test_snapaligner_index { SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[]) diff --git a/tests/modules/nf-core/snippy/core/main.nf b/tests/modules/nf-core/snippy/core/main.nf index be78d8bdf44..26949c8a575 100644 --- a/tests/modules/nf-core/snippy/core/main.nf +++ b/tests/modules/nf-core/snippy/core/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf' -include { SNIPPY_CORE } from '../../../../modules/snippy/core/main.nf' +include { SNIPPY_RUN } from '../../../../modules/nf-core/snippy/run/main.nf' +include { SNIPPY_CORE } from '../../../../modules/nf-core/snippy/core/main.nf' workflow test_snippy_core { diff --git a/tests/modules/nf-core/snippy/run/main.nf b/tests/modules/nf-core/snippy/run/main.nf index bfc4082e158..142fd091284 100644 --- a/tests/modules/nf-core/snippy/run/main.nf +++ b/tests/modules/nf-core/snippy/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf' +include { SNIPPY_RUN } from '../../../../modules/nf-core/snippy/run/main.nf' workflow test_snippy_run { diff --git a/tests/modules/nf-core/snpdists/main.nf b/tests/modules/nf-core/snpdists/main.nf index be6d745c451..625b3ddd3cb 100644 --- a/tests/modules/nf-core/snpdists/main.nf +++ b/tests/modules/nf-core/snpdists/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPDISTS } from '../../../modules/snpdists/main.nf' +include { SNPDISTS } from '../../../modules/nf-core/snpdists/main.nf' workflow test_snpdists { diff --git a/tests/modules/nf-core/snpeff/main.nf b/tests/modules/nf-core/snpeff/main.nf index 81c44c105b2..23b3cdbcc97 100644 --- a/tests/modules/nf-core/snpeff/main.nf +++ b/tests/modules/nf-core/snpeff/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPEFF } from '../../../modules/snpeff/main.nf' +include { SNPEFF } from '../../../modules/nf-core/snpeff/main.nf' workflow test_snpeff { input = [ diff --git a/tests/modules/nf-core/snpsift/split/main.nf b/tests/modules/nf-core/snpsift/split/main.nf index 4579fee32f8..2431840a4c8 100644 --- a/tests/modules/nf-core/snpsift/split/main.nf +++ b/tests/modules/nf-core/snpsift/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPSIFT_SPLIT } from '../../../../modules/snpsift/split/main.nf' +include { SNPSIFT_SPLIT } from '../../../../modules/nf-core/snpsift/split/main.nf' workflow test_snpsift_split_base { diff --git a/tests/modules/nf-core/snpsites/main.nf b/tests/modules/nf-core/snpsites/main.nf index f780167393f..25e0051d500 100644 --- a/tests/modules/nf-core/snpsites/main.nf +++ b/tests/modules/nf-core/snpsites/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPSITES } from '../../../modules/snpsites/main.nf' +include { SNPSITES } from '../../../modules/nf-core/snpsites/main.nf' workflow test_snpsites { diff --git a/tests/modules/nf-core/somalier/extract/main.nf b/tests/modules/nf-core/somalier/extract/main.nf index 3b56e0653f4..cc47c1f4ff6 100644 --- a/tests/modules/nf-core/somalier/extract/main.nf +++ b/tests/modules/nf-core/somalier/extract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SOMALIER_EXTRACT } from '../../../../modules/somalier/extract/main.nf' +include { SOMALIER_EXTRACT } from '../../../../modules/nf-core/somalier/extract/main.nf' fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/somalier/relate/main.nf b/tests/modules/nf-core/somalier/relate/main.nf index 030e5b2a175..2387fe6837b 100644 --- a/tests/modules/nf-core/somalier/relate/main.nf +++ b/tests/modules/nf-core/somalier/relate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SOMALIER_RELATE } from '../../../../modules/somalier/relate/main.nf' +include { SOMALIER_RELATE } from '../../../../modules/nf-core/somalier/relate/main.nf' workflow test_somalier_relate { diff --git a/tests/modules/nf-core/sourmash/sketch/main.nf b/tests/modules/nf-core/sourmash/sketch/main.nf index c9288c593e4..49fd0ce1df9 100644 --- a/tests/modules/nf-core/sourmash/sketch/main.nf +++ b/tests/modules/nf-core/sourmash/sketch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SOURMASH_SKETCH } from '../../../../modules/sourmash/sketch/main.nf' +include { SOURMASH_SKETCH } from '../../../../modules/nf-core/sourmash/sketch/main.nf' workflow test_sourmash_sketch { diff --git a/tests/modules/nf-core/spades/main.nf b/tests/modules/nf-core/spades/main.nf index 3710eeb716c..58b07bc9647 100644 --- a/tests/modules/nf-core/spades/main.nf +++ b/tests/modules/nf-core/spades/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SPADES } from '../../../modules/spades/main.nf' +include { SPADES } from '../../../modules/nf-core/spades/main.nf' workflow test_spades_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/spatyper/main.nf b/tests/modules/nf-core/spatyper/main.nf index 655845c72f0..62a7e0c5ebe 100644 --- a/tests/modules/nf-core/spatyper/main.nf +++ b/tests/modules/nf-core/spatyper/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SPATYPER } from '../../../modules/spatyper/main.nf' -include { SPATYPER as SPATYPER_ENRICH } from '../../../modules/spatyper/main.nf' +include { SPATYPER } from '../../../modules/nf-core/spatyper/main.nf' +include { SPATYPER as SPATYPER_ENRICH } from '../../../modules/nf-core/spatyper/main.nf' workflow test_spatyper { input = [ [ id:'test' ], diff --git a/tests/modules/nf-core/sratools/fasterqdump/main.nf b/tests/modules/nf-core/sratools/fasterqdump/main.nf index daa7a5aee13..57984ccb1b8 100644 --- a/tests/modules/nf-core/sratools/fasterqdump/main.nf +++ b/tests/modules/nf-core/sratools/fasterqdump/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/untar/main.nf' -include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { SRATOOLS_FASTERQDUMP } from '../../../../modules/nf-core/sratools/fasterqdump/main.nf' workflow test_sratools_fasterqdump_single_end { diff --git a/tests/modules/nf-core/sratools/prefetch/main.nf b/tests/modules/nf-core/sratools/prefetch/main.nf index cf9794abea5..cd59e61567b 100644 --- a/tests/modules/nf-core/sratools/prefetch/main.nf +++ b/tests/modules/nf-core/sratools/prefetch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf' +include { SRATOOLS_PREFETCH } from '../../../../modules/nf-core/sratools/prefetch/main.nf' workflow test_sratools_prefetch { diff --git a/tests/modules/nf-core/srst2/srst2/main.nf b/tests/modules/nf-core/srst2/srst2/main.nf index 7d51937b848..aaeed0178c8 100644 --- a/tests/modules/nf-core/srst2/srst2/main.nf +++ b/tests/modules/nf-core/srst2/srst2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf' +include { SRST2_SRST2 } from '../../../../modules/nf-core/srst2/srst2/main.nf' workflow test_srst2_srst2_exit { diff --git a/tests/modules/nf-core/ssuissero/main.nf b/tests/modules/nf-core/ssuissero/main.nf index aa285133c83..ff744cc3ca8 100644 --- a/tests/modules/nf-core/ssuissero/main.nf +++ b/tests/modules/nf-core/ssuissero/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SSUISSERO } from '../../../modules/ssuissero/main.nf' +include { SSUISSERO } from '../../../modules/nf-core/ssuissero/main.nf' workflow test_ssuissero { diff --git a/tests/modules/nf-core/stadeniolib/scramble/main.nf b/tests/modules/nf-core/stadeniolib/scramble/main.nf index d29c6dd8292..15ce8382d50 100644 --- a/tests/modules/nf-core/stadeniolib/scramble/main.nf +++ b/tests/modules/nf-core/stadeniolib/scramble/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STADENIOLIB_SCRAMBLE } from '../../../../modules/stadeniolib/scramble/main.nf' +include { STADENIOLIB_SCRAMBLE } from '../../../../modules/nf-core/stadeniolib/scramble/main.nf' workflow test_stadeniolib { diff --git a/tests/modules/nf-core/staphopiasccmec/main.nf b/tests/modules/nf-core/staphopiasccmec/main.nf index 8ea310ce38f..13d30a376ca 100644 --- a/tests/modules/nf-core/staphopiasccmec/main.nf +++ b/tests/modules/nf-core/staphopiasccmec/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { STAPHOPIASCCMEC } from '../../../modules/staphopiasccmec/main.nf' -include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../modules/staphopiasccmec/main.nf' +include { STAPHOPIASCCMEC } from '../../../modules/nf-core/staphopiasccmec/main.nf' +include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../modules/nf-core/staphopiasccmec/main.nf' workflow test_staphopiasccmec { diff --git a/tests/modules/nf-core/star/align/main.nf b/tests/modules/nf-core/star/align/main.nf index bf305d5412e..a13e9805233 100644 --- a/tests/modules/nf-core/star/align/main.nf +++ b/tests/modules/nf-core/star/align/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' -include { STAR_ALIGN } from '../../../../modules/star/align/main.nf' -include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/star/align/main.nf' -include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/star/align/main.nf' +include { STAR_GENOMEGENERATE } from '../../../../modules/nf-core/star/genomegenerate/main.nf' +include { STAR_ALIGN } from '../../../../modules/nf-core/star/align/main.nf' +include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/nf-core/star/align/main.nf' +include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/nf-core/star/align/main.nf' workflow test_star_alignment_single_end { input = [ diff --git a/tests/modules/nf-core/star/genomegenerate/main.nf b/tests/modules/nf-core/star/genomegenerate/main.nf index 316014784d5..072fc37db60 100644 --- a/tests/modules/nf-core/star/genomegenerate/main.nf +++ b/tests/modules/nf-core/star/genomegenerate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' +include { STAR_GENOMEGENERATE } from '../../../../modules/nf-core/star/genomegenerate/main.nf' workflow test_star_genomegenerate { fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/stranger/main.nf b/tests/modules/nf-core/stranger/main.nf index 4a930c19ce6..edd977947fd 100644 --- a/tests/modules/nf-core/stranger/main.nf +++ b/tests/modules/nf-core/stranger/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf' -include { STRANGER } from '../../../modules/stranger/main.nf' +include { EXPANSIONHUNTER } from '../../../modules/nf-core/expansionhunter/main.nf' +include { STRANGER } from '../../../modules/nf-core/stranger/main.nf' input = [ [ id:'test', gender:'male' ], // meta map diff --git a/tests/modules/nf-core/strelka/germline/main.nf b/tests/modules/nf-core/strelka/germline/main.nf index 312a4f720a2..c6ee89eb654 100644 --- a/tests/modules/nf-core/strelka/germline/main.nf +++ b/tests/modules/nf-core/strelka/germline/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf' +include { STRELKA_GERMLINE } from '../../../../modules/nf-core/strelka/germline/main.nf' workflow test_strelka_germline { input = [ diff --git a/tests/modules/nf-core/strelka/somatic/main.nf b/tests/modules/nf-core/strelka/somatic/main.nf index ab75f0e2012..0d796f3f4e2 100644 --- a/tests/modules/nf-core/strelka/somatic/main.nf +++ b/tests/modules/nf-core/strelka/somatic/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRELKA_SOMATIC } from '../../../../modules/strelka/somatic/main.nf' +include { STRELKA_SOMATIC } from '../../../../modules/nf-core/strelka/somatic/main.nf' workflow test_strelka_somatic { diff --git a/tests/modules/nf-core/stringtie/merge/main.nf b/tests/modules/nf-core/stringtie/merge/main.nf index 3fe32902595..86c5ba1c0de 100644 --- a/tests/modules/nf-core/stringtie/merge/main.nf +++ b/tests/modules/nf-core/stringtie/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' -include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' +include { STRINGTIE_STRINGTIE } from '../../../../modules/nf-core/stringtie/stringtie/main.nf' +include { STRINGTIE_MERGE } from '../../../../modules/nf-core/stringtie/merge/main.nf' /* * Test with forward strandedness diff --git a/tests/modules/nf-core/stringtie/stringtie/main.nf b/tests/modules/nf-core/stringtie/stringtie/main.nf index 463e4b98183..633877714a7 100644 --- a/tests/modules/nf-core/stringtie/stringtie/main.nf +++ b/tests/modules/nf-core/stringtie/stringtie/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' +include { STRINGTIE_STRINGTIE } from '../../../../modules/nf-core/stringtie/stringtie/main.nf' // // Test with forward strandedness // diff --git a/tests/modules/nf-core/subread/featurecounts/main.nf b/tests/modules/nf-core/subread/featurecounts/main.nf index a8fa5c755ed..722debaa614 100644 --- a/tests/modules/nf-core/subread/featurecounts/main.nf +++ b/tests/modules/nf-core/subread/featurecounts/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SUBREAD_FEATURECOUNTS } from '../../../../modules/subread/featurecounts/main.nf' +include { SUBREAD_FEATURECOUNTS } from '../../../../modules/nf-core/subread/featurecounts/main.nf' workflow test_subread_featurecounts_forward { diff --git a/tests/modules/nf-core/svdb/merge/main.nf b/tests/modules/nf-core/svdb/merge/main.nf index 3cbb4b44544..f320df78507 100644 --- a/tests/modules/nf-core/svdb/merge/main.nf +++ b/tests/modules/nf-core/svdb/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SVDB_MERGE } from '../../../../modules/svdb/merge/main.nf' +include { SVDB_MERGE } from '../../../../modules/nf-core/svdb/merge/main.nf' workflow test_svdb_merge { diff --git a/tests/modules/nf-core/svdb/query/main.nf b/tests/modules/nf-core/svdb/query/main.nf index c014320f09f..66b37d14096 100644 --- a/tests/modules/nf-core/svdb/query/main.nf +++ b/tests/modules/nf-core/svdb/query/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SVDB_QUERY } from '../../../../modules/svdb/query/main.nf' +include { SVDB_QUERY } from '../../../../modules/nf-core/svdb/query/main.nf' workflow test_svdb_query { diff --git a/tests/modules/nf-core/svtk/standardize/main.nf b/tests/modules/nf-core/svtk/standardize/main.nf index 6601edbd456..97a1b3d14aa 100644 --- a/tests/modules/nf-core/svtk/standardize/main.nf +++ b/tests/modules/nf-core/svtk/standardize/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SVTK_STANDARDIZE } from '../../../../modules/svtk/standardize/main.nf' -include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf' +include { SVTK_STANDARDIZE } from '../../../../modules/nf-core/svtk/standardize/main.nf' +include { MANTA_GERMLINE } from '../../../../modules/nf-core/manta/germline/main.nf' workflow test_svtk_standardize { diff --git a/tests/modules/nf-core/tabix/bgzip/main.nf b/tests/modules/nf-core/tabix/bgzip/main.nf index 1be82fa5d16..65c6ba1ce15 100644 --- a/tests/modules/nf-core/tabix/bgzip/main.nf +++ b/tests/modules/nf-core/tabix/bgzip/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { TABIX_BGZIP } from '../../../../modules/tabix/bgzip/main.nf' -include { TABIX_BGZIP as TABIX_BGZIP_WITH_GZI } from '../../../../modules/tabix/bgzip/main.nf' +include { TABIX_BGZIP } from '../../../../modules/nf-core/tabix/bgzip/main.nf' +include { TABIX_BGZIP as TABIX_BGZIP_WITH_GZI } from '../../../../modules/nf-core/tabix/bgzip/main.nf' workflow test_tabix_bgzip_compress { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/tabix/bgziptabix/main.nf b/tests/modules/nf-core/tabix/bgziptabix/main.nf index b2ff70d0175..f9eec7e2507 100644 --- a/tests/modules/nf-core/tabix/bgziptabix/main.nf +++ b/tests/modules/nf-core/tabix/bgziptabix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main.nf' +include { TABIX_BGZIPTABIX } from '../../../../modules/nf-core/tabix/bgziptabix/main.nf' workflow test_tabix_bgziptabix { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/tabix/tabix/main.nf b/tests/modules/nf-core/tabix/tabix/main.nf index da26f4d7ef5..1653e60173f 100644 --- a/tests/modules/nf-core/tabix/tabix/main.nf +++ b/tests/modules/nf-core/tabix/tabix/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_BED } from '../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/nf-core/tabix/tabix/main.nf' workflow test_tabix_tabix_bed { input = [ [ id:'B.bed' ], // meta map diff --git a/tests/modules/nf-core/tailfindr/main.nf b/tests/modules/nf-core/tailfindr/main.nf index a5c3b7d94b0..2102527fda0 100644 --- a/tests/modules/nf-core/tailfindr/main.nf +++ b/tests/modules/nf-core/tailfindr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TAILFINDR } from '../../../modules/tailfindr/main.nf' +include { TAILFINDR } from '../../../modules/nf-core/tailfindr/main.nf' workflow test_tailfindr { diff --git a/tests/modules/nf-core/tbprofiler/profile/main.nf b/tests/modules/nf-core/tbprofiler/profile/main.nf index 0141a77fad2..8495f6b7ed8 100644 --- a/tests/modules/nf-core/tbprofiler/profile/main.nf +++ b/tests/modules/nf-core/tbprofiler/profile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TBPROFILER_PROFILE } from '../../../../modules/tbprofiler/profile/main.nf' +include { TBPROFILER_PROFILE } from '../../../../modules/nf-core/tbprofiler/profile/main.nf' workflow test_tbprofiler_profile_illumina { diff --git a/tests/modules/nf-core/tiddit/cov/main.nf b/tests/modules/nf-core/tiddit/cov/main.nf index 0032c759921..eea0b027c56 100644 --- a/tests/modules/nf-core/tiddit/cov/main.nf +++ b/tests/modules/nf-core/tiddit/cov/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/tiddit/cov/main.nf' -include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/tiddit/cov/main.nf' +include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/nf-core/tiddit/cov/main.nf' +include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/nf-core/tiddit/cov/main.nf' workflow test_tiddit_cov_cram_bed { diff --git a/tests/modules/nf-core/tiddit/sv/main.nf b/tests/modules/nf-core/tiddit/sv/main.nf index 2f944129dbf..ff08f3dfb07 100644 --- a/tests/modules/nf-core/tiddit/sv/main.nf +++ b/tests/modules/nf-core/tiddit/sv/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' -include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf' -include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/tiddit/sv/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { TIDDIT_SV } from '../../../../modules/nf-core/tiddit/sv/main.nf' +include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/nf-core/tiddit/sv/main.nf' workflow test_tiddit_sv_bam { input = [ diff --git a/tests/modules/nf-core/transdecoder/longorf/main.nf b/tests/modules/nf-core/transdecoder/longorf/main.nf index 90f75d193a9..6375ef7a724 100644 --- a/tests/modules/nf-core/transdecoder/longorf/main.nf +++ b/tests/modules/nf-core/transdecoder/longorf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TRANSDECODER_LONGORF } from '../../../../modules/transdecoder/longorf/main.nf' +include { TRANSDECODER_LONGORF } from '../../../../modules/nf-core/transdecoder/longorf/main.nf' workflow test_transdecoder_longorf { diff --git a/tests/modules/nf-core/transdecoder/predict/main.nf b/tests/modules/nf-core/transdecoder/predict/main.nf index 02026a37984..dbb6c021f30 100644 --- a/tests/modules/nf-core/transdecoder/predict/main.nf +++ b/tests/modules/nf-core/transdecoder/predict/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { TRANSDECODER_PREDICT } from '../../../../modules/transdecoder/predict/main.nf' -include { TRANSDECODER_LONGORF } from '../../../../modules/transdecoder/longorf/main.nf' +include { TRANSDECODER_PREDICT } from '../../../../modules/nf-core/transdecoder/predict/main.nf' +include { TRANSDECODER_LONGORF } from '../../../../modules/nf-core/transdecoder/longorf/main.nf' workflow test_transdecoder_predict { diff --git a/tests/modules/nf-core/trimgalore/main.nf b/tests/modules/nf-core/trimgalore/main.nf index adeda539eb8..db87ce77ea4 100644 --- a/tests/modules/nf-core/trimgalore/main.nf +++ b/tests/modules/nf-core/trimgalore/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TRIMGALORE } from '../../../modules/trimgalore/main.nf' +include { TRIMGALORE } from '../../../modules/nf-core/trimgalore/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/trimmomatic/main.nf b/tests/modules/nf-core/trimmomatic/main.nf index bd87f1b6120..9cd54fbddcb 100644 --- a/tests/modules/nf-core/trimmomatic/main.nf +++ b/tests/modules/nf-core/trimmomatic/main.nf @@ -4,7 +4,7 @@ include { TRIMMOMATIC as TRIMMOMATIC_SE TRIMMOMATIC as TRIMMOMATIC_PE TRIMMOMATIC -} from '../../../modules/trimmomatic/main.nf' +} from '../../../modules/nf-core/trimmomatic/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/ucsc/bedclip/main.nf b/tests/modules/nf-core/ucsc/bedclip/main.nf index 8ccfd3b0b5f..e6a5049df2c 100755 --- a/tests/modules/nf-core/ucsc/bedclip/main.nf +++ b/tests/modules/nf-core/ucsc/bedclip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDCLIP } from '../../../../modules/ucsc/bedclip/main.nf' +include { UCSC_BEDCLIP } from '../../../../modules/nf-core/ucsc/bedclip/main.nf' workflow test_ucsc_bedclip { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index c6db7225b74..5dade993f6e 100644 --- a/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../modules/ucsc/bedgraphtobigwig/main.nf' +include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../modules/nf-core/ucsc/bedgraphtobigwig/main.nf' workflow test_ucsc_bedgraphtobigwig { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/ucsc/bedtobigbed/main.nf b/tests/modules/nf-core/ucsc/bedtobigbed/main.nf index 36a9b423e2d..03de60c21fe 100644 --- a/tests/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/tests/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDTOBIGBED } from '../../../../modules/ucsc/bedtobigbed/main.nf' -include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../modules/ucsc/bedtobigbed/main.nf' +include { UCSC_BEDTOBIGBED } from '../../../../modules/nf-core/ucsc/bedtobigbed/main.nf' +include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../modules/nf-core/ucsc/bedtobigbed/main.nf' workflow test_ucsc_bedtobigbed { input = [ [ id: 'test' ], // meta map diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index 3b20dc32ef3..f48ff39a05f 100644 --- a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/ucsc/bigwigaverageoverbed/main.nf' +include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/nf-core/ucsc/bigwigaverageoverbed/main.nf' workflow test_ucsc_bigwigaverageoverbed { input = [ diff --git a/tests/modules/nf-core/ucsc/liftover/main.nf b/tests/modules/nf-core/ucsc/liftover/main.nf index 168193f4e31..9ee2e472483 100644 --- a/tests/modules/nf-core/ucsc/liftover/main.nf +++ b/tests/modules/nf-core/ucsc/liftover/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_LIFTOVER } from '../../../../modules/ucsc/liftover/main.nf' +include { UCSC_LIFTOVER } from '../../../../modules/nf-core/ucsc/liftover/main.nf' workflow test_ucsc_liftover { diff --git a/tests/modules/nf-core/ucsc/wigtobigwig/main.nf b/tests/modules/nf-core/ucsc/wigtobigwig/main.nf index 2abbe5b2609..33e23937dc3 100644 --- a/tests/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/tests/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_WIGTOBIGWIG } from '../../../../modules/ucsc/wigtobigwig/main.nf' +include { UCSC_WIGTOBIGWIG } from '../../../../modules/nf-core/ucsc/wigtobigwig/main.nf' workflow test_ucsc_wigtobigwig { diff --git a/tests/modules/nf-core/ultra/align/main.nf b/tests/modules/nf-core/ultra/align/main.nf index 14795077564..2d5bba382f7 100644 --- a/tests/modules/nf-core/ultra/align/main.nf +++ b/tests/modules/nf-core/ultra/align/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../../modules/gunzip/main.nf' -include { GFFREAD } from '../../../../modules/gffread/main.nf' -include { ULTRA_INDEX } from '../../../../modules/ultra/index/main.nf' -include { ULTRA_ALIGN } from '../../../../modules/ultra/align/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' +include { ULTRA_INDEX } from '../../../../modules/nf-core/ultra/index/main.nf' +include { ULTRA_ALIGN } from '../../../../modules/nf-core/ultra/align/main.nf' workflow test_ultra_align { diff --git a/tests/modules/nf-core/ultra/index/main.nf b/tests/modules/nf-core/ultra/index/main.nf index 82056b4762d..ce98ee7922d 100644 --- a/tests/modules/nf-core/ultra/index/main.nf +++ b/tests/modules/nf-core/ultra/index/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ULTRA_INDEX } from '../../../../modules/ultra/index/main.nf' -include { GFFREAD } from '../../../../modules/gffread/main.nf' +include { ULTRA_INDEX } from '../../../../modules/nf-core/ultra/index/main.nf' +include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' workflow test_ultra_index { diff --git a/tests/modules/nf-core/ultra/pipeline/main.nf b/tests/modules/nf-core/ultra/pipeline/main.nf index 483d48fcdab..dcd3bc4d585 100644 --- a/tests/modules/nf-core/ultra/pipeline/main.nf +++ b/tests/modules/nf-core/ultra/pipeline/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' -include { GUNZIP } from '../../../../modules/gunzip/main.nf' -include { GFFREAD } from '../../../../modules/gffread/main.nf' +include { ULTRA_PIPELINE } from '../../../../modules/nf-core/ultra/pipeline/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' workflow test_ultra_pipeline { diff --git a/tests/modules/nf-core/umitools/dedup/main.nf b/tests/modules/nf-core/umitools/dedup/main.nf index 1edcb287605..6478d619c78 100644 --- a/tests/modules/nf-core/umitools/dedup/main.nf +++ b/tests/modules/nf-core/umitools/dedup/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf' -include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' -include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf' -include { SAMTOOLS_INDEX } from '../../../../modules/samtools/index/main.nf' -include { UMITOOLS_DEDUP } from '../../../../modules/umitools/dedup/main.nf' +include { UMITOOLS_EXTRACT } from '../../../../modules/nf-core/umitools/extract/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM } from '../../../../modules/nf-core/bwa/mem/main.nf' +include { SAMTOOLS_INDEX } from '../../../../modules/nf-core/samtools/index/main.nf' +include { UMITOOLS_DEDUP } from '../../../../modules/nf-core/umitools/dedup/main.nf' // // Test with no UMI diff --git a/tests/modules/nf-core/umitools/extract/main.nf b/tests/modules/nf-core/umitools/extract/main.nf index 3baac16a8c6..b6301eece75 100644 --- a/tests/modules/nf-core/umitools/extract/main.nf +++ b/tests/modules/nf-core/umitools/extract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf' +include { UMITOOLS_EXTRACT } from '../../../../modules/nf-core/umitools/extract/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/unicycler/main.nf b/tests/modules/nf-core/unicycler/main.nf index 861b139bff5..c430a56efa9 100644 --- a/tests/modules/nf-core/unicycler/main.nf +++ b/tests/modules/nf-core/unicycler/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UNICYCLER } from '../../../modules/unicycler/main.nf' +include { UNICYCLER } from '../../../modules/nf-core/unicycler/main.nf' workflow test_unicycler_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/untar/main.nf b/tests/modules/nf-core/untar/main.nf index 079f3aebbb4..698f39e299e 100644 --- a/tests/modules/nf-core/untar/main.nf +++ b/tests/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../modules/untar/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' workflow test_untar { input = [ diff --git a/tests/modules/nf-core/unzip/main.nf b/tests/modules/nf-core/unzip/main.nf index 6f7cc030648..f20ad35d9c4 100644 --- a/tests/modules/nf-core/unzip/main.nf +++ b/tests/modules/nf-core/unzip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UNZIP } from '../../../modules/unzip/main.nf' +include { UNZIP } from '../../../modules/nf-core/unzip/main.nf' workflow test_unzip { diff --git a/tests/modules/nf-core/vardictjava/main.nf b/tests/modules/nf-core/vardictjava/main.nf index 557c5bbe8ae..0267bb4ee57 100644 --- a/tests/modules/nf-core/vardictjava/main.nf +++ b/tests/modules/nf-core/vardictjava/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf' +include { VARDICTJAVA } from '../../../modules/nf-core/vardictjava/main.nf' workflow test_vardictjava_bam { diff --git a/tests/modules/nf-core/variantbam/main.nf b/tests/modules/nf-core/variantbam/main.nf index 016a9104ba1..150e8e4c061 100644 --- a/tests/modules/nf-core/variantbam/main.nf +++ b/tests/modules/nf-core/variantbam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VARIANTBAM } from '../../../modules/variantbam/main.nf' +include { VARIANTBAM } from '../../../modules/nf-core/variantbam/main.nf' workflow test_variantbam { diff --git a/tests/modules/nf-core/vcf2db/main.nf b/tests/modules/nf-core/vcf2db/main.nf index 0d4be5d23e1..6ff2a64f570 100644 --- a/tests/modules/nf-core/vcf2db/main.nf +++ b/tests/modules/nf-core/vcf2db/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VCF2DB } from '../../../modules/vcf2db/main.nf' +include { VCF2DB } from '../../../modules/nf-core/vcf2db/main.nf' workflow test_vcf2db { diff --git a/tests/modules/nf-core/vcf2maf/main.nf b/tests/modules/nf-core/vcf2maf/main.nf index 57f3a6cb4c2..7d51739c786 100644 --- a/tests/modules/nf-core/vcf2maf/main.nf +++ b/tests/modules/nf-core/vcf2maf/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { VCF2MAF } from '../../../modules/vcf2maf/main.nf' -include { UNTAR } from '../../../modules/untar/main.nf' +include { VCF2MAF } from '../../../modules/nf-core/vcf2maf/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' workflow test_vcf2maf_no_vep { diff --git a/tests/modules/nf-core/vcfanno/main.nf b/tests/modules/nf-core/vcfanno/main.nf index a1fe7c1aba3..6f744be342a 100644 --- a/tests/modules/nf-core/vcfanno/main.nf +++ b/tests/modules/nf-core/vcfanno/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../modules/untar/main.nf' -include { VCFANNO } from '../../../modules/vcfanno/main.nf' +include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { VCFANNO } from '../../../modules/nf-core/vcfanno/main.nf' workflow test_vcfanno { diff --git a/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 7e973300dac..22703141a3d 100644 --- a/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VCFLIB_VCFBREAKMULTI } from '../../../../modules/vcflib/vcfbreakmulti/main.nf' +include { VCFLIB_VCFBREAKMULTI } from '../../../../modules/nf-core/vcflib/vcfbreakmulti/main.nf' workflow test_vcflib_vcfbreakmulti { diff --git a/tests/modules/nf-core/vcflib/vcfuniq/main.nf b/tests/modules/nf-core/vcflib/vcfuniq/main.nf index f2c8e6f89f2..d920d97d39b 100644 --- a/tests/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/tests/modules/nf-core/vcflib/vcfuniq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VCFLIB_VCFUNIQ } from '../../../../modules/vcflib/vcfuniq/main.nf' +include { VCFLIB_VCFUNIQ } from '../../../../modules/nf-core/vcflib/vcfuniq/main.nf' workflow test_vcflib_vcfuniq { diff --git a/tests/modules/nf-core/vcftools/main.nf b/tests/modules/nf-core/vcftools/main.nf index 21f9aa88481..a7659f3b143 100644 --- a/tests/modules/nf-core/vcftools/main.nf +++ b/tests/modules/nf-core/vcftools/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { VCFTOOLS as VCFTOOLS_BASE } from '../../../modules/vcftools/main.nf' -include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/vcftools/main.nf' +include { VCFTOOLS as VCFTOOLS_BASE } from '../../../modules/nf-core/vcftools/main.nf' +include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/nf-core/vcftools/main.nf' workflow test_vcftools_vcf_base { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf b/tests/modules/nf-core/vsearch/sintax/main.nf index 14112f0bf9c..0f80c599c7e 100644 --- a/tests/modules/nf-core/vsearch/sintax/main.nf +++ b/tests/modules/nf-core/vsearch/sintax/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VSEARCH_SINTAX } from '../../../../modules/vsearch/sintax/main.nf' +include { VSEARCH_SINTAX } from '../../../../modules/nf-core/vsearch/sintax/main.nf' workflow test_vsearch_sintax { diff --git a/tests/modules/nf-core/vsearch/usearchglobal/main.nf b/tests/modules/nf-core/vsearch/usearchglobal/main.nf index 90dc31917f6..252269136c7 100644 --- a/tests/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/tests/modules/nf-core/vsearch/usearchglobal/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VSEARCH_USEARCHGLOBAL } from '../../../../modules/vsearch/usearchglobal/main.nf' +include { VSEARCH_USEARCHGLOBAL } from '../../../../modules/nf-core/vsearch/usearchglobal/main.nf' workflow test_vsearch_usearchglobal { diff --git a/tests/modules/nf-core/whamg/main.nf b/tests/modules/nf-core/whamg/main.nf index 82561f58e79..22e8ab7b643 100644 --- a/tests/modules/nf-core/whamg/main.nf +++ b/tests/modules/nf-core/whamg/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { WHAMG } from '../../../modules/whamg/main.nf' +include { WHAMG } from '../../../modules/nf-core/whamg/main.nf' workflow test_whamg_bam { diff --git a/tests/modules/nf-core/yara/index/main.nf b/tests/modules/nf-core/yara/index/main.nf index 89eb0f7de25..c0de4cd844f 100644 --- a/tests/modules/nf-core/yara/index/main.nf +++ b/tests/modules/nf-core/yara/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' +include { YARA_INDEX } from '../../../../modules/nf-core/yara/index/main.nf' workflow test_yara_index { diff --git a/tests/modules/nf-core/yara/mapper/main.nf b/tests/modules/nf-core/yara/mapper/main.nf index 18800eb3194..3279c3c735b 100644 --- a/tests/modules/nf-core/yara/mapper/main.nf +++ b/tests/modules/nf-core/yara/mapper/main.nf @@ -3,8 +3,8 @@ nextflow.enable.dsl = 2 -include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' -include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf' +include { YARA_INDEX } from '../../../../modules/nf-core/yara/index/main.nf' +include { YARA_MAPPER } from '../../../../modules/nf-core/yara/mapper/main.nf' workflow test_yara_single_end { From 9c349328a1c71bfaf83adf28fbbc7f2fca12472a Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 18:59:44 +0100 Subject: [PATCH 4/9] Replace relative paths in subworkflow main scripts --- subworkflows/nf-core/align_bowtie2/main.nf | 2 +- subworkflows/nf-core/bam_qc_picard/main.nf | 6 +++--- subworkflows/nf-core/bam_sort_samtools/main.nf | 4 ++-- .../nf-core/bam_stats_samtools/main.nf | 6 +++--- .../nf-core/fgbio_create_umi_consensus/main.nf | 18 +++++++++--------- .../nf-core/gatk_create_som_pon/main.nf | 6 +++--- .../main.nf | 12 ++++++------ .../main.nf | 8 ++++---- subworkflows/nf-core/srafastq/main.nf | 6 +++--- 9 files changed, 34 insertions(+), 34 deletions(-) diff --git a/subworkflows/nf-core/align_bowtie2/main.nf b/subworkflows/nf-core/align_bowtie2/main.nf index ec453f8d317..d6d7cd60d4e 100644 --- a/subworkflows/nf-core/align_bowtie2/main.nf +++ b/subworkflows/nf-core/align_bowtie2/main.nf @@ -7,7 +7,7 @@ params.samtools_sort_options = [:] params.samtools_index_options = [:] params.samtools_stats_options = [:] -include { BOWTIE2_ALIGN } from '../../../modules/bowtie2/align/main' addParams( options: params.align_options ) +include { BOWTIE2_ALIGN } from '../../../modules/nf-core/bowtie2/align/main' addParams( options: params.align_options ) include { BAM_SORT_SAMTOOLS } from '../bam_sort_samtools/main' addParams( sort_options: params.samtools_sort_options, index_options: params.samtools_index_options, stats_options: params.samtools_stats_options ) workflow ALIGN_BOWTIE2 { diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf index e38697c3eb9..57ffa46bf3c 100644 --- a/subworkflows/nf-core/bam_qc_picard/main.nf +++ b/subworkflows/nf-core/bam_qc_picard/main.nf @@ -2,9 +2,9 @@ // Run QC steps on BAM/CRAM files using Picard // -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main' -include { PICARD_COLLECTWGSMETRICS } from '../../../modules/picard/collectwgsmetrics/main' -include { PICARD_COLLECTHSMETRICS } from '../../../modules/picard/collecthsmetrics/main' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' +include { PICARD_COLLECTWGSMETRICS } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' workflow BAM_QC_PICARD { take: diff --git a/subworkflows/nf-core/bam_sort_samtools/main.nf b/subworkflows/nf-core/bam_sort_samtools/main.nf index c9be6a56e47..fc1a24df51a 100644 --- a/subworkflows/nf-core/bam_sort_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_samtools/main.nf @@ -6,8 +6,8 @@ params.sort_options = [:] params.index_options = [:] params.stats_options = [:] -include { SAMTOOLS_SORT } from '../../../modules/samtools/sort/main' addParams( options: params.sort_options ) -include { SAMTOOLS_INDEX } from '../../../modules/samtools/index/main' addParams( options: params.index_options ) +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' addParams( options: params.sort_options ) +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' addParams( options: params.index_options ) include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' addParams( options: params.stats_options ) workflow BAM_SORT_SAMTOOLS { diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf index 188894a2ab9..f4fab25bc8a 100644 --- a/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -2,9 +2,9 @@ // Run SAMtools stats, flagstat and idxstats // -include { SAMTOOLS_STATS } from '../../../modules/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' workflow BAM_STATS_SAMTOOLS { take: diff --git a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf index 042d0bbd5e1..41aa787d953 100644 --- a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf +++ b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf @@ -5,15 +5,15 @@ // -include { BWAMEM2_INDEX } from '../../../modules/bwamem2/index/main.nf' -include { BWAMEM2_MEM } from '../../../modules/bwamem2/mem/main' -include { BWA_INDEX as BWAMEM1_INDEX } from '../../../modules/bwa/index/main.nf' -include { BWA_MEM as BWAMEM1_MEM } from '../../../modules/bwa/mem/main' -include { FGBIO_CALLMOLECULARCONSENSUSREADS as CALLUMICONSENSUS } from '../../../modules/fgbio/callmolecularconsensusreads/main.nf' -include { FGBIO_FASTQTOBAM as FASTQTOBAM } from '../../../modules/fgbio/fastqtobam/main' -include { FGBIO_GROUPREADSBYUMI as GROUPREADSBYUMI } from '../../../modules/fgbio/groupreadsbyumi/main' -include { SAMBLASTER } from '../../../modules/samblaster/main' -include { SAMTOOLS_BAM2FQ as BAM2FASTQ } from '../../../modules/samtools/bam2fq/main.nf' +include { BWAMEM2_INDEX } from '../../../modules/nf-core/bwamem2/index/main.nf' +include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main' +include { BWA_INDEX as BWAMEM1_INDEX } from '../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM as BWAMEM1_MEM } from '../../../modules/nf-core/bwa/mem/main' +include { FGBIO_CALLMOLECULARCONSENSUSREADS as CALLUMICONSENSUS } from '../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf' +include { FGBIO_FASTQTOBAM as FASTQTOBAM } from '../../../modules/nf-core/fgbio/fastqtobam/main' +include { FGBIO_GROUPREADSBYUMI as GROUPREADSBYUMI } from '../../../modules/nf-core/fgbio/groupreadsbyumi/main' +include { SAMBLASTER } from '../../../modules/nf-core/samblaster/main' +include { SAMTOOLS_BAM2FQ as BAM2FASTQ } from '../../../modules/nf-core/samtools/bam2fq/main.nf' workflow CREATE_UMI_CONSENSUS { diff --git a/subworkflows/nf-core/gatk_create_som_pon/main.nf b/subworkflows/nf-core/gatk_create_som_pon/main.nf index 89a9566ee36..544289bcc8f 100644 --- a/subworkflows/nf-core/gatk_create_som_pon/main.nf +++ b/subworkflows/nf-core/gatk_create_som_pon/main.nf @@ -5,9 +5,9 @@ params.mutect2_options = [args: '--max-mnp-distance 0'] params.gendbimport_options = [:] params.createsompon_options = [:] -include { GATK4_MUTECT2 } from '../../../modules/gatk4/mutect2/main' addParams( options: params.mutect2_options ) -include { GATK4_GENOMICSDBIMPORT } from '../../../modules/gatk4/genomicsdbimport/main' addParams( options: params.gendbimport_options ) -include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../modules/gatk4/createsomaticpanelofnormals/main' addParams( options: params.createsompon_options ) +include { GATK4_MUTECT2 } from '../../../modules/nf-core/gatk4/mutect2/main' addParams( options: params.mutect2_options ) +include { GATK4_GENOMICSDBIMPORT } from '../../../modules/nf-core/gatk4/genomicsdbimport/main' addParams( options: params.gendbimport_options ) +include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main' addParams( options: params.createsompon_options ) workflow GATK_CREATE_SOM_PON { take: diff --git a/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf index 25c63687d78..81b543a9437 100644 --- a/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf @@ -9,12 +9,12 @@ params.getpileup_normal_options = [suffix: '_normal'] params.calccontam_options = [:] params.filtercalls_options = [suffix: '_filtered'] -include { GATK4_MUTECT2 as MUTECT2 } from '../../../modules/gatk4/mutect2/main' addParams( options: params.mutect2_options ) -include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../modules/gatk4/learnreadorientationmodel/main' addParams( options: params.learnorientation_options ) -include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES_TUMOR } from '../../../modules/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_tumor_options ) -include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES_NORMAL} from '../../../modules/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_normal_options ) -include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION } from '../../../modules/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options ) -include { GATK4_FILTERMUTECTCALLS as FILTERMUTECTCALLS } from '../../../modules/gatk4/filtermutectcalls/main' addParams( options: params.filtercalls_options ) +include { GATK4_MUTECT2 as MUTECT2 } from '../../../modules/nf-core/gatk4/mutect2/main' addParams( options: params.mutect2_options ) +include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../modules/nf-core/gatk4/learnreadorientationmodel/main' addParams( options: params.learnorientation_options ) +include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES_TUMOR } from '../../../modules/nf-core/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_tumor_options ) +include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES_NORMAL} from '../../../modules/nf-core/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_normal_options ) +include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION } from '../../../modules/nf-core/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options ) +include { GATK4_FILTERMUTECTCALLS as FILTERMUTECTCALLS } from '../../../modules/nf-core/gatk4/filtermutectcalls/main' addParams( options: params.filtercalls_options ) workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING { take: diff --git a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf index 20d8a176bab..ca3d78ff6d6 100644 --- a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main.nf @@ -7,10 +7,10 @@ params.getpileup_options = [:] params.calccontam_options = [:] params.filtercalls_options = [suffix: '_filtered'] -include { GATK4_MUTECT2 as MUTECT2 } from '../../../modules/gatk4/mutect2/main' addParams( options: params.mutect2_options ) -include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES } from '../../../modules/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_options ) -include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION } from '../../../modules/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options ) -include { GATK4_FILTERMUTECTCALLS as FILTERMUTECTCALLS } from '../../../modules/gatk4/filtermutectcalls/main' addParams( options: params.filtercalls_options ) +include { GATK4_MUTECT2 as MUTECT2 } from '../../../modules/nf-core/gatk4/mutect2/main' addParams( options: params.mutect2_options ) +include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES } from '../../../modules/nf-core/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_options ) +include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION } from '../../../modules/nf-core/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options ) +include { GATK4_FILTERMUTECTCALLS as FILTERMUTECTCALLS } from '../../../modules/nf-core/gatk4/filtermutectcalls/main' addParams( options: params.filtercalls_options ) workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING { take: diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/srafastq/main.nf index 26e8105eb6e..af52066243b 100644 --- a/subworkflows/nf-core/srafastq/main.nf +++ b/subworkflows/nf-core/srafastq/main.nf @@ -1,6 +1,6 @@ -include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main' -include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main' -include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main' +include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/custom/sratoolsncbisettings/main' +include { SRATOOLS_PREFETCH } from '../../../modules/nf-core/sratools/prefetch/main' +include { SRATOOLS_FASTERQDUMP } from '../../../modules/nf-core/sratools/fasterqdump/main' /** * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA). From 7bde27f1f08c3d2bdf434f5d96ce09c2872974a2 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 19:01:00 +0100 Subject: [PATCH 5/9] Replace relative paths in subworkflow test scripts --- tests/subworkflows/nf-core/align_bowtie2/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/subworkflows/nf-core/align_bowtie2/main.nf b/tests/subworkflows/nf-core/align_bowtie2/main.nf index 9870242d4af..160c1bf3c95 100644 --- a/tests/subworkflows/nf-core/align_bowtie2/main.nf +++ b/tests/subworkflows/nf-core/align_bowtie2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [:] ) +include { BOWTIE2_BUILD } from '../../../../modules/nf-core/bowtie2/build/main.nf' addParams( options: [:] ) include { ALIGN_BOWTIE2 } from '../../../../subworkflows/nf-core/align_bowtie2/main.nf' addParams( 'samtools_sort_options': ['suffix': '.sorted'] ) workflow test_align_bowtie2_single_end { From 6c2ca083e8c73cba37abf333ccb2772169efbbc3 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 19:07:42 +0100 Subject: [PATCH 6/9] Replace paths to tests in test.yml --- tests/modules/nf-core/abacas/test.yml | 2 +- tests/modules/nf-core/abricate/run/test.yml | 2 +- .../modules/nf-core/abricate/summary/test.yml | 2 +- tests/modules/nf-core/adapterremoval/test.yml | 6 +++--- .../nf-core/adapterremovalfixprefix/test.yml | 2 +- tests/modules/nf-core/agrvate/test.yml | 2 +- tests/modules/nf-core/allelecounter/test.yml | 4 ++-- tests/modules/nf-core/ampir/test.yml | 2 +- .../modules/nf-core/amplify/predict/test.yml | 2 +- tests/modules/nf-core/amps/test.yml | 2 +- .../nf-core/amrfinderplus/run/test.yml | 2 +- .../nf-core/amrfinderplus/update/test.yml | 2 +- tests/modules/nf-core/angsd/docounts/test.yml | 2 +- .../nf-core/antismash/antismashlite/test.yml | 2 +- .../antismashlitedownloaddatabases/test.yml | 2 +- tests/modules/nf-core/ariba/getref/test.yml | 2 +- tests/modules/nf-core/ariba/run/test.yml | 2 +- tests/modules/nf-core/arriba/test.yml | 4 ++-- .../modules/nf-core/artic/guppyplex/test.yml | 2 +- tests/modules/nf-core/artic/minion/test.yml | 2 +- tests/modules/nf-core/ascat/test.yml | 2 +- tests/modules/nf-core/assemblyscan/test.yml | 2 +- tests/modules/nf-core/ataqv/ataqv/test.yml | 10 +++++----- tests/modules/nf-core/ataqv/mkarv/test.yml | 2 +- tests/modules/nf-core/atlas/call/test.yml | 2 +- tests/modules/nf-core/atlas/pmd/test.yml | 2 +- tests/modules/nf-core/atlas/recal/test.yml | 2 +- .../modules/nf-core/atlas/splitmerge/test.yml | 2 +- tests/modules/nf-core/bakta/test.yml | 2 +- .../modules/nf-core/bamaligncleaner/test.yml | 2 +- tests/modules/nf-core/bamcmp/test.yml | 2 +- .../modules/nf-core/bamtools/convert/test.yml | 18 ++++++++--------- tests/modules/nf-core/bamtools/split/test.yml | 4 ++-- tests/modules/nf-core/bamtools/stats/test.yml | 2 +- .../modules/nf-core/bamutil/trimbam/test.yml | 2 +- tests/modules/nf-core/bandage/image/test.yml | 2 +- tests/modules/nf-core/bases2fastq/test.yml | 2 +- tests/modules/nf-core/bbmap/align/test.yml | 8 ++++---- tests/modules/nf-core/bbmap/bbduk/test.yml | 8 ++++---- tests/modules/nf-core/bbmap/bbsplit/test.yml | 2 +- tests/modules/nf-core/bbmap/clumpify/test.yml | 4 ++-- tests/modules/nf-core/bbmap/index/test.yml | 2 +- tests/modules/nf-core/bbmap/pileup/test.yml | 2 +- .../nf-core/bcftools/annotate/test.yml | 4 ++-- .../modules/nf-core/bcftools/concat/test.yml | 4 ++-- .../nf-core/bcftools/consensus/test.yml | 2 +- .../modules/nf-core/bcftools/convert/test.yml | 6 +++--- .../modules/nf-core/bcftools/filter/test.yml | 2 +- tests/modules/nf-core/bcftools/index/test.yml | 4 ++-- tests/modules/nf-core/bcftools/isec/test.yml | 2 +- tests/modules/nf-core/bcftools/merge/test.yml | 8 ++++---- .../modules/nf-core/bcftools/mpileup/test.yml | 4 ++-- tests/modules/nf-core/bcftools/norm/test.yml | 4 ++-- tests/modules/nf-core/bcftools/query/test.yml | 4 ++-- .../nf-core/bcftools/reheader/test.yml | 6 +++--- tests/modules/nf-core/bcftools/roh/test.yml | 4 ++-- tests/modules/nf-core/bcftools/sort/test.yml | 2 +- tests/modules/nf-core/bcftools/stats/test.yml | 6 +++--- tests/modules/nf-core/bcftools/view/test.yml | 4 ++-- tests/modules/nf-core/bcl2fastq/test.yml | 2 +- tests/modules/nf-core/bclconvert/test.yml | 2 +- .../nf-core/bedtools/bamtobed/test.yml | 2 +- .../nf-core/bedtools/complement/test.yml | 2 +- .../nf-core/bedtools/genomecov/test.yml | 8 ++++---- .../nf-core/bedtools/getfasta/test.yml | 2 +- .../nf-core/bedtools/intersect/test.yml | 4 ++-- .../nf-core/bedtools/makewindows/test.yml | 2 +- .../nf-core/bedtools/maskfasta/test.yml | 2 +- tests/modules/nf-core/bedtools/merge/test.yml | 2 +- tests/modules/nf-core/bedtools/slop/test.yml | 2 +- tests/modules/nf-core/bedtools/sort/test.yml | 2 +- tests/modules/nf-core/bedtools/split/test.yml | 2 +- .../nf-core/bedtools/subtract/test.yml | 2 +- .../biobambam/bammarkduplicates2/test.yml | 2 +- .../nf-core/biobambam/bammerge/test.yml | 4 ++-- .../nf-core/biobambam/bamsormadup/test.yml | 4 ++-- tests/modules/nf-core/biscuit/align/test.yml | 4 ++-- .../nf-core/biscuit/biscuitblaster/test.yml | 4 ++-- tests/modules/nf-core/biscuit/bsconv/test.yml | 2 +- .../modules/nf-core/biscuit/epiread/test.yml | 6 +++--- tests/modules/nf-core/biscuit/index/test.yml | 2 +- .../modules/nf-core/biscuit/mergecg/test.yml | 2 +- tests/modules/nf-core/biscuit/pileup/test.yml | 4 ++-- tests/modules/nf-core/biscuit/qc/test.yml | 2 +- .../modules/nf-core/biscuit/vcf2bed/test.yml | 2 +- tests/modules/nf-core/bismark/align/test.yml | 4 ++-- .../nf-core/bismark/deduplicate/test.yml | 2 +- .../bismark/genomepreparation/test.yml | 2 +- .../bismark/methylationextractor/test.yml | 2 +- tests/modules/nf-core/bismark/report/test.yml | 2 +- .../modules/nf-core/bismark/summary/test.yml | 2 +- tests/modules/nf-core/blast/blastn/test.yml | 2 +- .../nf-core/blast/makeblastdb/test.yml | 2 +- tests/modules/nf-core/blast/tblastn/test.yml | 2 +- tests/modules/nf-core/bowtie/align/test.yml | 4 ++-- .../nf-core/bowtie/build_test/test.yml | 2 +- tests/modules/nf-core/bowtie2/align/test.yml | 10 +++++----- .../nf-core/bowtie2/build_test/test.yml | 2 +- .../modules/nf-core/bracken/bracken/test.yml | 8 ++++---- .../bracken/combinebrackenoutputs/test.yml | 2 +- tests/modules/nf-core/busco/test.yml | 12 +++++------ tests/modules/nf-core/bwa/aln/test.yml | 4 ++-- tests/modules/nf-core/bwa/index/test.yml | 2 +- tests/modules/nf-core/bwa/mem/test.yml | 8 ++++---- tests/modules/nf-core/bwa/sampe/test.yml | 2 +- tests/modules/nf-core/bwa/samse/test.yml | 2 +- tests/modules/nf-core/bwamem2/index/test.yml | 2 +- tests/modules/nf-core/bwamem2/mem/test.yml | 8 ++++---- tests/modules/nf-core/bwameth/align/test.yml | 4 ++-- tests/modules/nf-core/bwameth/index/test.yml | 2 +- tests/modules/nf-core/cat/cat/test.yml | 20 +++++++++---------- tests/modules/nf-core/cat/fastq/test.yml | 18 ++++++++--------- .../modules/nf-core/cellranger/count/test.yml | 2 +- .../nf-core/cellranger/mkfastq/test.yml | 4 ++-- .../modules/nf-core/cellranger/mkgtf/test.yml | 2 +- .../modules/nf-core/cellranger/mkref/test.yml | 2 +- .../nf-core/centrifuge/centrifuge/test.yml | 4 ++-- .../nf-core/centrifuge/kreport/test.yml | 4 ++-- .../modules/nf-core/checkm/lineagewf/test.yml | 4 ++-- tests/modules/nf-core/checkm/qa/test.yml | 4 ++-- .../modules/nf-core/chromap/chromap/test.yml | 6 +++--- tests/modules/nf-core/chromap/index/test.yml | 2 +- tests/modules/nf-core/clonalframeml/test.yml | 2 +- tests/modules/nf-core/cmseq/polymut/test.yml | 6 +++--- .../nf-core/cnvkit/antitarget/test.yml | 2 +- tests/modules/nf-core/cnvkit/batch/test.yml | 14 ++++++------- .../modules/nf-core/cnvkit/reference/test.yml | 2 +- .../nf-core/cnvpytor/callcnvs/test.yml | 4 ++-- .../nf-core/cnvpytor/histogram/test.yml | 4 ++-- .../nf-core/cnvpytor/importreaddepth/test.yml | 8 ++++---- .../nf-core/cnvpytor/partition/test.yml | 4 ++-- tests/modules/nf-core/cnvpytor/view/test.yml | 6 +++--- .../controlfreec/assesssignificance/test.yml | 4 ++-- .../nf-core/controlfreec/freec/test.yml | 4 ++-- .../nf-core/controlfreec/freec2bed/test.yml | 4 ++-- .../controlfreec/freec2circos/test.yml | 4 ++-- .../nf-core/controlfreec/makegraph/test.yml | 4 ++-- tests/modules/nf-core/cooler/cload/test.yml | 6 +++--- tests/modules/nf-core/cooler/digest/test.yml | 2 +- tests/modules/nf-core/cooler/dump/test.yml | 2 +- tests/modules/nf-core/cooler/merge/test.yml | 2 +- tests/modules/nf-core/cooler/zoomify/test.yml | 2 +- tests/modules/nf-core/csvtk/concat/test.yml | 2 +- tests/modules/nf-core/csvtk/split/test.yml | 4 ++-- .../custom/dumpsoftwareversions/test.yml | 2 +- .../nf-core/custom/getchromsizes/test.yml | 4 ++-- .../custom/sratoolsncbisettings/test.yml | 6 +++--- tests/modules/nf-core/cutadapt/test.yml | 4 ++-- tests/modules/nf-core/damageprofiler/test.yml | 6 +++--- .../modules/nf-core/dastool/dastool/test.yml | 2 +- .../dastool/fastatocontig2bin/test.yml | 4 ++-- .../nf-core/dastool/scaffolds2bin/test.yml | 4 ++-- tests/modules/nf-core/dedup/test.yml | 2 +- .../nf-core/deeparg/downloaddata/test.yml | 2 +- .../modules/nf-core/deeparg/predict/test.yml | 2 +- .../modules/nf-core/deepbgc/download/test.yml | 2 +- .../modules/nf-core/deepbgc/pipeline/test.yml | 4 ++-- .../nf-core/deeptools/bamcoverage/test.yml | 6 +++--- .../nf-core/deeptools/computematrix/test.yml | 2 +- .../deeptools/plotfingerprint/test.yml | 2 +- .../nf-core/deeptools/plotheatmap/test.yml | 2 +- .../nf-core/deeptools/plotprofile/test.yml | 2 +- tests/modules/nf-core/deepvariant/test.yml | 4 ++-- tests/modules/nf-core/delly/call/test.yml | 6 +++--- tests/modules/nf-core/diamond/blastp/test.yml | 4 ++-- tests/modules/nf-core/diamond/blastx/test.yml | 4 ++-- tests/modules/nf-core/diamond/makedb/test.yml | 2 +- tests/modules/nf-core/dragmap/align/test.yml | 8 ++++---- .../nf-core/dragmap/hashtable/test.yml | 2 +- tests/modules/nf-core/dragonflye/test.yml | 4 ++-- .../nf-core/dshbio/exportsegments/test.yml | 8 ++++---- .../modules/nf-core/dshbio/filterbed/test.yml | 2 +- .../nf-core/dshbio/filtergff3/test.yml | 2 +- .../modules/nf-core/dshbio/splitbed/test.yml | 2 +- .../modules/nf-core/dshbio/splitgff3/test.yml | 2 +- tests/modules/nf-core/ectyper/test.yml | 2 +- tests/modules/nf-core/eido/convert/test.yml | 4 ++-- tests/modules/nf-core/eido/validate/test.yml | 4 ++-- tests/modules/nf-core/elprep/filter/test.yml | 2 +- tests/modules/nf-core/elprep/merge/test.yml | 2 +- tests/modules/nf-core/elprep/split/test.yml | 2 +- tests/modules/nf-core/emboss/seqret/test.yml | 8 ++++---- tests/modules/nf-core/emmtyper/test.yml | 2 +- tests/modules/nf-core/endorspy/test.yml | 2 +- tests/modules/nf-core/ensemblvep/test.yml | 16 +++++++-------- .../nf-core/entrezdirect/esearch/test.yml | 6 +++--- .../nf-core/entrezdirect/esummary/test.yml | 6 +++--- .../nf-core/entrezdirect/xtract/test.yml | 4 ++-- tests/modules/nf-core/epang/test.yml | 2 +- .../modules/nf-core/expansionhunter/test.yml | 2 +- tests/modules/nf-core/faqcs/test.yml | 4 ++-- tests/modules/nf-core/fargene/test.yml | 2 +- tests/modules/nf-core/fastani/test.yml | 2 +- tests/modules/nf-core/fastawindows/test.yml | 2 +- tests/modules/nf-core/fastk/fastk/test.yml | 4 ++-- tests/modules/nf-core/fastk/histex/test.yml | 2 +- tests/modules/nf-core/fastk/merge/test.yml | 4 ++-- tests/modules/nf-core/fastp/test.yml | 12 +++++------ tests/modules/nf-core/fastqc/test.yml | 4 ++-- tests/modules/nf-core/fastqscan/test.yml | 2 +- tests/modules/nf-core/fasttree/test.yml | 2 +- tests/modules/nf-core/fcs/fcsadaptor/test.yml | 2 +- tests/modules/nf-core/ffq/test.yml | 4 ++-- .../callmolecularconsensusreads/test.yml | 2 +- .../modules/nf-core/fgbio/fastqtobam/test.yml | 12 +++++------ .../nf-core/fgbio/groupreadsbyumi/test.yml | 2 +- tests/modules/nf-core/fgbio/sortbam/test.yml | 2 +- tests/modules/nf-core/filtlong/test.yml | 6 +++--- tests/modules/nf-core/flash/test.yml | 2 +- tests/modules/nf-core/flye/test.yml | 12 +++++------ tests/modules/nf-core/fq/lint/test.yml | 4 ++-- tests/modules/nf-core/freebayes/test.yml | 10 +++++----- tests/modules/nf-core/gamma/gamma/test.yml | 4 ++-- .../nf-core/gappa/examineassign/test.yml | 2 +- .../nf-core/gappa/examinegraft/test.yml | 2 +- .../nf-core/gappa/examineheattree/test.yml | 2 +- .../nf-core/gatk/indelrealigner/test.yml | 2 +- .../gatk/realignertargetcreator/test.yml | 2 +- .../nf-core/gatk/unifiedgenotyper/test.yml | 2 +- .../modules/nf-core/gatk4/applybqsr/test.yml | 6 +++--- .../nf-core/gatk4/applybqsrspark/test.yml | 6 +++--- .../modules/nf-core/gatk4/applyvqsr/test.yml | 4 ++-- .../nf-core/gatk4/baserecalibrator/test.yml | 8 ++++---- .../gatk4/baserecalibratorspark/test.yml | 8 ++++---- .../nf-core/gatk4/bedtointervallist/test.yml | 2 +- .../gatk4/calculatecontamination/test.yml | 6 +++--- .../gatk4/calibratedragstrmodel/test.yml | 6 +++--- .../nf-core/gatk4/cnnscorevariants/test.yml | 2 +- .../nf-core/gatk4/collectreadcounts/test.yml | 6 +++--- .../nf-core/gatk4/collectsvevidence/test.yml | 6 +++--- .../nf-core/gatk4/combinegvcfs/test.yml | 2 +- .../gatk4/composestrtablefile/test.yml | 2 +- .../gatk4/createsequencedictionary/test.yml | 2 +- .../createsomaticpanelofnormals/test.yml | 2 +- .../gatk4/estimatelibrarycomplexity/test.yml | 2 +- .../modules/nf-core/gatk4/fastqtosam/test.yml | 4 ++-- .../nf-core/gatk4/filtermutectcalls/test.yml | 8 ++++---- .../gatk4/filtervarianttranches/test.yml | 2 +- .../nf-core/gatk4/gatherbqsrreports/test.yml | 4 ++-- .../gatk4/gatherpileupsummaries/test.yml | 2 +- .../nf-core/gatk4/genomicsdbimport/test.yml | 6 +++--- .../nf-core/gatk4/genotypegvcfs/test.yml | 18 ++++++++--------- .../nf-core/gatk4/getpileupsummaries/test.yml | 4 ++-- 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| 4 ++-- tests/modules/nf-core/mapdamage2/test.yml | 2 +- tests/modules/nf-core/mash/dist/test.yml | 2 +- tests/modules/nf-core/mash/screen/test.yml | 2 +- tests/modules/nf-core/mash/sketch/test.yml | 2 +- tests/modules/nf-core/mashtree/test.yml | 2 +- tests/modules/nf-core/maxbin2/test.yml | 2 +- tests/modules/nf-core/maxquant/lfq/test.yml | 2 +- tests/modules/nf-core/mcroni/test.yml | 2 +- tests/modules/nf-core/md5sum/test.yml | 2 +- tests/modules/nf-core/medaka/test.yml | 2 +- tests/modules/nf-core/megahit/test.yml | 4 ++-- tests/modules/nf-core/megan/daa2info/test.yml | 2 +- tests/modules/nf-core/megan/rma2info/test.yml | 2 +- tests/modules/nf-core/meningotype/test.yml | 2 +- tests/modules/nf-core/merqury/test.yml | 2 +- .../nf-core/merquryfk/katcomp/test.yml | 4 ++-- .../modules/nf-core/merquryfk/katgc/test.yml | 4 ++-- .../nf-core/merquryfk/merquryfk/test.yml | 4 ++-- .../nf-core/merquryfk/ploidyplot/test.yml | 4 ++-- tests/modules/nf-core/meryl/count/test.yml | 4 ++-- 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+++--- .../modules/nf-core/samtools/mpileup/test.yml | 4 ++-- tests/modules/nf-core/samtools/sort/test.yml | 2 +- tests/modules/nf-core/samtools/stats/test.yml | 4 ++-- tests/modules/nf-core/samtools/view/test.yml | 12 +++++------ tests/modules/nf-core/scoary/test.yml | 2 +- .../nf-core/scramble/clusteranalysis/test.yml | 4 ++-- .../scramble/clusteridentifier/test.yml | 4 ++-- tests/modules/nf-core/seacr/callpeak/test.yml | 4 ++-- tests/modules/nf-core/seqkit/pair/test.yml | 2 +- tests/modules/nf-core/seqkit/replace/test.yml | 4 ++-- tests/modules/nf-core/seqkit/split2/test.yml | 12 +++++------ tests/modules/nf-core/seqkit/stats/test.yml | 10 +++++----- tests/modules/nf-core/seqsero2/test.yml | 2 +- tests/modules/nf-core/seqtk/mergepe/test.yml | 4 ++-- tests/modules/nf-core/seqtk/rename/test.yml | 4 ++-- tests/modules/nf-core/seqtk/sample/test.yml | 4 ++-- tests/modules/nf-core/seqtk/seq/test.yml | 4 ++-- tests/modules/nf-core/seqtk/subseq/test.yml | 2 +- .../nf-core/sequenzautils/bam2seqz/test.yml | 2 +- .../nf-core/sequenzautils/gcwiggle/test.yml | 2 +- tests/modules/nf-core/seqwish/induce/test.yml | 4 ++-- tests/modules/nf-core/seroba/run/test.yml | 2 +- tests/modules/nf-core/sexdeterrmine/test.yml | 2 +- tests/modules/nf-core/shasta/test.yml | 2 +- tests/modules/nf-core/shasum/test.yml | 2 +- tests/modules/nf-core/shigatyper/test.yml | 6 +++--- tests/modules/nf-core/shovill/test.yml | 8 ++++---- tests/modules/nf-core/sistr/test.yml | 2 +- tests/modules/nf-core/slimfastq/test.yml | 8 ++++---- .../nf-core/snapaligner/align/test.yml | 4 ++-- .../nf-core/snapaligner/index/test.yml | 2 +- tests/modules/nf-core/snippy/core/test.yml | 2 +- tests/modules/nf-core/snippy/run/test.yml | 2 +- tests/modules/nf-core/snpdists/test.yml | 2 +- tests/modules/nf-core/snpeff/test.yml | 2 +- tests/modules/nf-core/snpsift/split/test.yml | 6 +++--- tests/modules/nf-core/snpsites/test.yml | 2 +- .../modules/nf-core/somalier/extract/test.yml | 2 +- .../modules/nf-core/somalier/relate/test.yml | 4 ++-- .../modules/nf-core/sourmash/sketch/test.yml | 2 +- tests/modules/nf-core/spades/test.yml | 8 ++++---- tests/modules/nf-core/spatyper/test.yml | 4 ++-- .../nf-core/sratools/fasterqdump/test.yml | 4 ++-- .../nf-core/sratools/prefetch/test.yml | 2 +- tests/modules/nf-core/srst2/srst2/test.yml | 8 ++++---- tests/modules/nf-core/ssuissero/test.yml | 2 +- .../nf-core/stadeniolib/scramble/test.yml | 2 +- .../modules/nf-core/staphopiasccmec/test.yml | 4 ++-- tests/modules/nf-core/star/align/test.yml | 10 +++++----- .../nf-core/star/genomegenerate/test.yml | 4 ++-- tests/modules/nf-core/stranger/test.yml | 6 +++--- .../modules/nf-core/strelka/germline/test.yml | 4 ++-- .../modules/nf-core/strelka/somatic/test.yml | 4 ++-- .../modules/nf-core/stringtie/merge/test.yml | 8 ++++---- .../nf-core/stringtie/stringtie/test.yml | 8 ++++---- .../nf-core/subread/featurecounts/test.yml | 6 +++--- tests/modules/nf-core/svdb/merge/test.yml | 6 +++--- tests/modules/nf-core/svdb/query/test.yml | 4 ++-- .../modules/nf-core/svtk/standardize/test.yml | 4 ++-- tests/modules/nf-core/tabix/bgzip/test.yml | 6 +++--- .../modules/nf-core/tabix/bgziptabix/test.yml | 2 +- tests/modules/nf-core/tabix/tabix/test.yml | 8 ++++---- tests/modules/nf-core/tailfindr/test.yml | 2 +- .../nf-core/tbprofiler/profile/test.yml | 4 ++-- tests/modules/nf-core/tiddit/cov/test.yml | 8 ++++---- tests/modules/nf-core/tiddit/sv/test.yml | 8 ++++---- .../nf-core/transdecoder/longorf/test.yml | 2 +- .../nf-core/transdecoder/predict/test.yml | 2 +- tests/modules/nf-core/trimgalore/test.yml | 4 ++-- tests/modules/nf-core/trimmomatic/test.yml | 6 +++--- tests/modules/nf-core/ucsc/bedclip/test.yml | 2 +- .../nf-core/ucsc/bedgraphtobigwig/test.yml | 2 +- .../modules/nf-core/ucsc/bedtobigbed/test.yml | 4 ++-- .../ucsc/bigwigaverageoverbed/test.yml | 2 +- tests/modules/nf-core/ucsc/liftover/test.yml | 2 +- .../modules/nf-core/ucsc/wigtobigwig/test.yml | 4 ++-- tests/modules/nf-core/ultra/align/test.yml | 2 +- tests/modules/nf-core/ultra/index/test.yml | 2 +- tests/modules/nf-core/ultra/pipeline/test.yml | 2 +- tests/modules/nf-core/umitools/dedup/test.yml | 8 ++++---- .../modules/nf-core/umitools/extract/test.yml | 4 ++-- tests/modules/nf-core/unicycler/test.yml | 6 +++--- tests/modules/nf-core/untar/test.yml | 6 +++--- tests/modules/nf-core/unzip/test.yml | 2 +- tests/modules/nf-core/vardictjava/test.yml | 2 +- tests/modules/nf-core/variantbam/test.yml | 2 +- tests/modules/nf-core/vcf2db/test.yml | 2 +- tests/modules/nf-core/vcf2maf/test.yml | 4 ++-- tests/modules/nf-core/vcfanno/test.yml | 4 ++-- .../nf-core/vcflib/vcfbreakmulti/test.yml | 4 ++-- tests/modules/nf-core/vcflib/vcfuniq/test.yml | 2 +- tests/modules/nf-core/vcftools/test.yml | 8 ++++---- tests/modules/nf-core/vsearch/sintax/test.yml | 2 +- .../nf-core/vsearch/usearchglobal/test.yml | 4 ++-- tests/modules/nf-core/whamg/test.yml | 2 +- tests/modules/nf-core/yara/index/test.yml | 2 +- tests/modules/nf-core/yara/mapper/test.yml | 4 ++-- 632 files changed, 1106 insertions(+), 1106 deletions(-) diff --git a/tests/modules/nf-core/abacas/test.yml b/tests/modules/nf-core/abacas/test.yml index c466a6ed958..3856b63a54d 100644 --- a/tests/modules/nf-core/abacas/test.yml +++ b/tests/modules/nf-core/abacas/test.yml @@ -1,5 +1,5 @@ - name: abacas - command: nextflow run ./tests/modules/abacas -entry test_abacas -c ./tests/config/nextflow.config -c ./tests/modules/abacas/nextflow.config + command: nextflow run ./tests/modules/nf-core/abacas -entry test_abacas -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/abacas/nextflow.config tags: - abacas files: diff --git a/tests/modules/nf-core/abricate/run/test.yml b/tests/modules/nf-core/abricate/run/test.yml index 3377623ccc3..809dd888d74 100644 --- a/tests/modules/nf-core/abricate/run/test.yml +++ b/tests/modules/nf-core/abricate/run/test.yml @@ -1,5 +1,5 @@ - name: abricate run - command: nextflow run tests/modules/abricate/run -entry test_abricate_run -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/abricate/run -entry test_abricate_run -c tests/config/nextflow.config tags: - abricate - abricate/run diff --git a/tests/modules/nf-core/abricate/summary/test.yml b/tests/modules/nf-core/abricate/summary/test.yml index abbd747be50..6c110b8ce6f 100644 --- a/tests/modules/nf-core/abricate/summary/test.yml +++ b/tests/modules/nf-core/abricate/summary/test.yml @@ -1,5 +1,5 @@ - name: abricate summary - command: nextflow run tests/modules/abricate/summary -entry test_abricate_summary -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/abricate/summary -entry test_abricate_summary -c tests/config/nextflow.config tags: - abricate - abricate/summary diff --git a/tests/modules/nf-core/adapterremoval/test.yml b/tests/modules/nf-core/adapterremoval/test.yml index e660da767fe..63aafa5f77a 100644 --- a/tests/modules/nf-core/adapterremoval/test.yml +++ b/tests/modules/nf-core/adapterremoval/test.yml @@ -1,5 +1,5 @@ - name: adapterremoval test_adapterremoval_single_end - command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config tags: - adapterremoval files: @@ -12,7 +12,7 @@ md5sum: ac5b46719719b7ee62739530b80869fc - name: adapterremoval test_adapterremoval_paired_end - command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config tags: - adapterremoval files: @@ -27,7 +27,7 @@ md5sum: fa621c887897da5a379c719399c17db7 - name: adapterremoval test_adapterremoval_paired_end_collapse - command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config tags: - adapterremoval files: diff --git a/tests/modules/nf-core/adapterremovalfixprefix/test.yml b/tests/modules/nf-core/adapterremovalfixprefix/test.yml index 4d4b72e7f8e..8e7de8c72b2 100644 --- a/tests/modules/nf-core/adapterremovalfixprefix/test.yml +++ b/tests/modules/nf-core/adapterremovalfixprefix/test.yml @@ -1,5 +1,5 @@ - name: adapterremovalfixprefix test_adapterremovalfixprefix - command: nextflow run tests/modules/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config tags: - adapterremovalfixprefix files: diff --git a/tests/modules/nf-core/agrvate/test.yml b/tests/modules/nf-core/agrvate/test.yml index 36e8886c8d7..04f9fabdafd 100644 --- a/tests/modules/nf-core/agrvate/test.yml +++ b/tests/modules/nf-core/agrvate/test.yml @@ -1,5 +1,5 @@ - name: agrvate - command: nextflow run ./tests/modules/agrvate -entry test_agrvate -c ./tests/config/nextflow.config -c ./tests/modules/agrvate/nextflow.config + command: nextflow run ./tests/modules/nf-core/agrvate -entry test_agrvate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/agrvate/nextflow.config tags: - agrvate files: diff --git a/tests/modules/nf-core/allelecounter/test.yml b/tests/modules/nf-core/allelecounter/test.yml index a0afbc1250a..048b0d572d1 100644 --- a/tests/modules/nf-core/allelecounter/test.yml +++ b/tests/modules/nf-core/allelecounter/test.yml @@ -1,5 +1,5 @@ - name: allelecounter test_allelecounter_bam - command: nextflow run ./tests/modules/allelecounter -entry test_allelecounter_bam -c ./tests/config/nextflow.config -c ./tests/modules/allelecounter/nextflow.config + command: nextflow run ./tests/modules/nf-core/allelecounter -entry test_allelecounter_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/allelecounter/nextflow.config tags: - allelecounter files: @@ -7,7 +7,7 @@ md5sum: 2bbe9d7331b78bdac30fe30dbc5fdaf3 - name: allelecounter test_allelecounter_cram - command: nextflow run ./tests/modules/allelecounter -entry test_allelecounter_cram -c ./tests/config/nextflow.config -c ./tests/modules/allelecounter/nextflow.config + command: nextflow run ./tests/modules/nf-core/allelecounter -entry test_allelecounter_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/allelecounter/nextflow.config tags: - allelecounter files: diff --git a/tests/modules/nf-core/ampir/test.yml b/tests/modules/nf-core/ampir/test.yml index 54921e9a32a..549dad70a43 100644 --- a/tests/modules/nf-core/ampir/test.yml +++ b/tests/modules/nf-core/ampir/test.yml @@ -1,5 +1,5 @@ - name: ampir test_ampir - command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config -c ./tests/modules/ampir/nextflow.config + command: nextflow run ./tests/modules/nf-core/ampir -entry test_ampir -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ampir/nextflow.config tags: - ampir files: diff --git a/tests/modules/nf-core/amplify/predict/test.yml b/tests/modules/nf-core/amplify/predict/test.yml index 3bc92889cea..285475def61 100644 --- a/tests/modules/nf-core/amplify/predict/test.yml +++ b/tests/modules/nf-core/amplify/predict/test.yml @@ -1,5 +1,5 @@ - name: amplify predict amplify_predict - command: nextflow run tests/modules/amplify/predict -entry amplify_predict -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/amplify/predict -entry amplify_predict -c tests/config/nextflow.config tags: - amplify/predict - amplify diff --git a/tests/modules/nf-core/amps/test.yml b/tests/modules/nf-core/amps/test.yml index f38320e4bef..80773184a18 100644 --- a/tests/modules/nf-core/amps/test.yml +++ b/tests/modules/nf-core/amps/test.yml @@ -1,5 +1,5 @@ - name: amps - command: nextflow run ./tests/modules/amps -entry test_amps -c ./tests/config/nextflow.config -c ./tests/modules/amps/nextflow.config + command: nextflow run ./tests/modules/nf-core/amps -entry test_amps -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/amps/nextflow.config tags: - amps files: diff --git a/tests/modules/nf-core/amrfinderplus/run/test.yml b/tests/modules/nf-core/amrfinderplus/run/test.yml index 0529fe13a3c..09e9d4d69a3 100644 --- a/tests/modules/nf-core/amrfinderplus/run/test.yml +++ b/tests/modules/nf-core/amrfinderplus/run/test.yml @@ -1,5 +1,5 @@ - name: amrfinderplus run test_amrfinderplus_run - command: nextflow run ./tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c ./tests/config/nextflow.config -c ./tests/modules/amrfinderplus/run/nextflow.config + command: nextflow run ./tests/modules/nf-core/amrfinderplus/run -entry test_amrfinderplus_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/amrfinderplus/run/nextflow.config tags: - amrfinderplus - amrfinderplus/run diff --git a/tests/modules/nf-core/amrfinderplus/update/test.yml b/tests/modules/nf-core/amrfinderplus/update/test.yml index df26973b309..b201dab695e 100644 --- a/tests/modules/nf-core/amrfinderplus/update/test.yml +++ b/tests/modules/nf-core/amrfinderplus/update/test.yml @@ -1,5 +1,5 @@ - name: amrfinderplus update test_amrfinderplus_update - command: nextflow run tests/modules/amrfinderplus/update -entry test_amrfinderplus_update -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/amrfinderplus/update -entry test_amrfinderplus_update -c tests/config/nextflow.config tags: - amrfinderplus - amrfinderplus/update diff --git a/tests/modules/nf-core/angsd/docounts/test.yml b/tests/modules/nf-core/angsd/docounts/test.yml index 7b7a9e583b0..eea06d7bcc5 100644 --- a/tests/modules/nf-core/angsd/docounts/test.yml +++ b/tests/modules/nf-core/angsd/docounts/test.yml @@ -1,5 +1,5 @@ - name: angsd docounts test_angsd_docounts - command: nextflow run ./tests/modules/angsd/docounts -entry test_angsd_docounts -c ./tests/config/nextflow.config -c ./tests/modules/angsd/docounts/nextflow.config + command: nextflow run ./tests/modules/nf-core/angsd/docounts -entry test_angsd_docounts -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/angsd/docounts/nextflow.config tags: - angsd/docounts - angsd diff --git a/tests/modules/nf-core/antismash/antismashlite/test.yml b/tests/modules/nf-core/antismash/antismashlite/test.yml index 4642319c362..e64ba816f1e 100644 --- a/tests/modules/nf-core/antismash/antismashlite/test.yml +++ b/tests/modules/nf-core/antismash/antismashlite/test.yml @@ -1,5 +1,5 @@ - name: antismash antismashlite test_antismashlite - command: nextflow run tests/modules/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config tags: - antismash/antismashlite - antismash diff --git a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml index b4a964a0b9b..c21f8128144 100644 --- a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml @@ -1,5 +1,5 @@ - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases - command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config tags: - antismash/antismashlitedownloaddatabases - antismash diff --git a/tests/modules/nf-core/ariba/getref/test.yml b/tests/modules/nf-core/ariba/getref/test.yml index 7fcef3f7668..7f67b0a8acc 100644 --- a/tests/modules/nf-core/ariba/getref/test.yml +++ b/tests/modules/nf-core/ariba/getref/test.yml @@ -1,5 +1,5 @@ - name: ariba getref test_ariba_getref - command: nextflow run ./tests/modules/ariba/getref -entry test_ariba_getref -c ./tests/config/nextflow.config -c ./tests/modules/ariba/getref/nextflow.config + command: nextflow run ./tests/modules/nf-core/ariba/getref -entry test_ariba_getref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ariba/getref/nextflow.config tags: - ariba - ariba/getref diff --git a/tests/modules/nf-core/ariba/run/test.yml b/tests/modules/nf-core/ariba/run/test.yml index c43b878f15a..fb4033fc47f 100644 --- a/tests/modules/nf-core/ariba/run/test.yml +++ b/tests/modules/nf-core/ariba/run/test.yml @@ -1,5 +1,5 @@ - name: ariba run test_ariba_run - command: nextflow run ./tests/modules/ariba/run -entry test_ariba_run -c ./tests/config/nextflow.config -c ./tests/modules/ariba/run/nextflow.config + command: nextflow run ./tests/modules/nf-core/ariba/run -entry test_ariba_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ariba/run/nextflow.config tags: - ariba - ariba/run diff --git a/tests/modules/nf-core/arriba/test.yml b/tests/modules/nf-core/arriba/test.yml index bdeab128db8..8110d08483d 100644 --- a/tests/modules/nf-core/arriba/test.yml +++ b/tests/modules/nf-core/arriba/test.yml @@ -1,5 +1,5 @@ - name: arriba test_arriba_single_end - command: nextflow run ./tests/modules/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/arriba/nextflow.config + command: nextflow run ./tests/modules/nf-core/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/nextflow.config tags: - arriba files: @@ -46,7 +46,7 @@ - path: output/star/test.SJ.out.tab - name: arriba test_arriba_paired_end - command: nextflow run ./tests/modules/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/arriba/nextflow.config + command: nextflow run ./tests/modules/nf-core/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/nextflow.config tags: - arriba files: diff --git a/tests/modules/nf-core/artic/guppyplex/test.yml b/tests/modules/nf-core/artic/guppyplex/test.yml index 6fd10898533..81514394350 100644 --- a/tests/modules/nf-core/artic/guppyplex/test.yml +++ b/tests/modules/nf-core/artic/guppyplex/test.yml @@ -1,5 +1,5 @@ - name: artic guppyplex - command: nextflow run ./tests/modules/artic/guppyplex -entry test_artic_guppyplex -c ./tests/config/nextflow.config -c ./tests/modules/artic/guppyplex/nextflow.config + command: nextflow run ./tests/modules/nf-core/artic/guppyplex -entry test_artic_guppyplex -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/artic/guppyplex/nextflow.config tags: - artic - artic/guppyplex diff --git a/tests/modules/nf-core/artic/minion/test.yml b/tests/modules/nf-core/artic/minion/test.yml index c8ad52d720f..fcc5fa171c7 100644 --- a/tests/modules/nf-core/artic/minion/test.yml +++ b/tests/modules/nf-core/artic/minion/test.yml @@ -1,5 +1,5 @@ - name: artic minion - command: nextflow run ./tests/modules/artic/minion -entry test_artic_minion -c ./tests/config/nextflow.config -c ./tests/modules/artic/minion/nextflow.config + command: nextflow run ./tests/modules/nf-core/artic/minion -entry test_artic_minion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/artic/minion/nextflow.config tags: - artic - artic/minion diff --git a/tests/modules/nf-core/ascat/test.yml b/tests/modules/nf-core/ascat/test.yml index 67479559472..2b97d948985 100644 --- a/tests/modules/nf-core/ascat/test.yml +++ b/tests/modules/nf-core/ascat/test.yml @@ -1,5 +1,5 @@ - name: ascat test_ascat - command: nextflow run tests/modules/ascat -entry test_ascat -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/ascat -entry test_ascat -c tests/config/nextflow.config -stub-run tags: - ascat files: diff --git a/tests/modules/nf-core/assemblyscan/test.yml b/tests/modules/nf-core/assemblyscan/test.yml index 4a3ba5ec52e..c1162f1f76a 100644 --- a/tests/modules/nf-core/assemblyscan/test.yml +++ b/tests/modules/nf-core/assemblyscan/test.yml @@ -1,5 +1,5 @@ - name: assemblyscan test_assemblyscan - command: nextflow run ./tests/modules/assemblyscan -entry test_assemblyscan -c ./tests/config/nextflow.config -c ./tests/modules/assemblyscan/nextflow.config + command: nextflow run ./tests/modules/nf-core/assemblyscan -entry test_assemblyscan -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/assemblyscan/nextflow.config tags: - assemblyscan files: diff --git a/tests/modules/nf-core/ataqv/ataqv/test.yml b/tests/modules/nf-core/ataqv/ataqv/test.yml index d46de34673e..921c3ec636c 100644 --- a/tests/modules/nf-core/ataqv/ataqv/test.yml +++ b/tests/modules/nf-core/ataqv/ataqv/test.yml @@ -1,5 +1,5 @@ - name: ataqv ataqv test_ataqv_ataqv - command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config + command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config tags: - ataqv - ataqv/ataqv @@ -9,7 +9,7 @@ - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_problem_reads - command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config + command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config tags: - ataqv - ataqv/ataqv @@ -20,7 +20,7 @@ - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_peak - command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_peak -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config + command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_peak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config tags: - ataqv - ataqv/ataqv @@ -30,7 +30,7 @@ - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_tss - command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_tss -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config + command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_tss -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config tags: - ataqv - ataqv/ataqv @@ -40,7 +40,7 @@ - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_excluded_regs - command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config + command: nextflow run ./tests/modules/nf-core/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/ataqv/nextflow.config tags: - ataqv - ataqv/ataqv diff --git a/tests/modules/nf-core/ataqv/mkarv/test.yml b/tests/modules/nf-core/ataqv/mkarv/test.yml index fc6e38018e0..184fac699e6 100644 --- a/tests/modules/nf-core/ataqv/mkarv/test.yml +++ b/tests/modules/nf-core/ataqv/mkarv/test.yml @@ -1,5 +1,5 @@ - name: ataqv mkarv test_ataqv_mkarv - command: nextflow run ./tests/modules/ataqv/mkarv -entry test_ataqv_mkarv -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/mkarv/nextflow.config + command: nextflow run ./tests/modules/nf-core/ataqv/mkarv -entry test_ataqv_mkarv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/mkarv/nextflow.config tags: - ataqv/mkarv - ataqv diff --git a/tests/modules/nf-core/atlas/call/test.yml b/tests/modules/nf-core/atlas/call/test.yml index b3e13951243..78549fa3feb 100644 --- a/tests/modules/nf-core/atlas/call/test.yml +++ b/tests/modules/nf-core/atlas/call/test.yml @@ -1,5 +1,5 @@ - name: atlas call test_atlas_call - command: nextflow run ./tests/modules/atlas/call -entry test_atlas_call -c ./tests/config/nextflow.config -c ./tests/modules/atlas/call/nextflow.config + command: nextflow run ./tests/modules/nf-core/atlas/call -entry test_atlas_call -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/call/nextflow.config tags: - atlas - atlas/call diff --git a/tests/modules/nf-core/atlas/pmd/test.yml b/tests/modules/nf-core/atlas/pmd/test.yml index 69e3def21a4..bb2c3f973ac 100644 --- a/tests/modules/nf-core/atlas/pmd/test.yml +++ b/tests/modules/nf-core/atlas/pmd/test.yml @@ -1,5 +1,5 @@ - name: atlas pmd test_atlas_pmd - command: nextflow run ./tests/modules/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config -c ./tests/modules/atlas/pmd/nextflow.config + command: nextflow run ./tests/modules/nf-core/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/pmd/nextflow.config tags: - atlas/pmd - atlas diff --git a/tests/modules/nf-core/atlas/recal/test.yml b/tests/modules/nf-core/atlas/recal/test.yml index 45bb87673bd..a18b22c01dc 100644 --- a/tests/modules/nf-core/atlas/recal/test.yml +++ b/tests/modules/nf-core/atlas/recal/test.yml @@ -1,5 +1,5 @@ - name: atlas recal test_atlas_recal - command: nextflow run ./tests/modules/atlas/recal -entry test_atlas_recal -c ./tests/config/nextflow.config -c ./tests/modules/atlas/recal/nextflow.config + command: nextflow run ./tests/modules/nf-core/atlas/recal -entry test_atlas_recal -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/recal/nextflow.config tags: - atlas/recal - atlas diff --git a/tests/modules/nf-core/atlas/splitmerge/test.yml b/tests/modules/nf-core/atlas/splitmerge/test.yml index 145a2e8ac48..e891f10dfed 100644 --- a/tests/modules/nf-core/atlas/splitmerge/test.yml +++ b/tests/modules/nf-core/atlas/splitmerge/test.yml @@ -1,5 +1,5 @@ - name: atlas splitmerge test_atlas_splitmerge - command: nextflow run tests/modules/atlas/splitmerge -entry test_atlas_splitmerge -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/atlas/splitmerge -entry test_atlas_splitmerge -c tests/config/nextflow.config tags: - atlas - atlas/splitmerge diff --git a/tests/modules/nf-core/bakta/test.yml b/tests/modules/nf-core/bakta/test.yml index 1eb3d8a5002..428a27d37ac 100644 --- a/tests/modules/nf-core/bakta/test.yml +++ b/tests/modules/nf-core/bakta/test.yml @@ -1,5 +1,5 @@ - name: bakta - command: nextflow run ./tests/modules/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run tags: - bakta files: diff --git a/tests/modules/nf-core/bamaligncleaner/test.yml b/tests/modules/nf-core/bamaligncleaner/test.yml index 4207b8c2873..a077d6124cb 100644 --- a/tests/modules/nf-core/bamaligncleaner/test.yml +++ b/tests/modules/nf-core/bamaligncleaner/test.yml @@ -1,5 +1,5 @@ - name: bamaligncleaner - command: nextflow run ./tests/modules/bamaligncleaner -entry test_bamaligncleaner -c ./tests/config/nextflow.config -c ./tests/modules/bamaligncleaner/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamaligncleaner -entry test_bamaligncleaner -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamaligncleaner/nextflow.config tags: - bamaligncleaner files: diff --git a/tests/modules/nf-core/bamcmp/test.yml b/tests/modules/nf-core/bamcmp/test.yml index 58fba458642..5d59fc3a892 100644 --- a/tests/modules/nf-core/bamcmp/test.yml +++ b/tests/modules/nf-core/bamcmp/test.yml @@ -1,5 +1,5 @@ - name: bamcmp test_bamcmp - command: nextflow run tests/modules/bamcmp -entry test_bamcmp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamcmp -entry test_bamcmp -c tests/config/nextflow.config tags: - bamcmp files: diff --git a/tests/modules/nf-core/bamtools/convert/test.yml b/tests/modules/nf-core/bamtools/convert/test.yml index 3922ece2357..16c70e03f1d 100644 --- a/tests/modules/nf-core/bamtools/convert/test.yml +++ b/tests/modules/nf-core/bamtools/convert/test.yml @@ -1,19 +1,19 @@ - name: bamtools convert test_bamtools_convert_ext_error - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config tags: - bamtools - bamtools/convert exit_code: 1 - name: bamtools convert test_bamtools_convert_noext_error - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config tags: - bamtools - bamtools/convert exit_code: 1 - name: bamtools convert test_bamtools_convert_bed - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -24,7 +24,7 @@ md5sum: eb7a144b8a97965d3482f6f96b8a8243 - name: bamtools convert test_bamtools_convert_fasta - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -35,7 +35,7 @@ md5sum: 42d19a2b2b07f05edb82b34369dfd754 - name: bamtools convert test_bamtools_convert_fastq - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -46,7 +46,7 @@ md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e - name: bamtools convert test_bamtools_convert_json - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -57,7 +57,7 @@ md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3 - name: bamtools convert test_bamtools_convert_pileup - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -68,7 +68,7 @@ md5sum: fd3ad0edd1e085b1a002e0593d1d5814 - name: bamtools convert test_bamtools_convert_sam - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -79,7 +79,7 @@ md5sum: 4be470ce3cc0143ae5ae415b612a4965 - name: bamtools convert test_bamtools_convert_yaml - command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config tags: - bamtools - bamtools/convert diff --git a/tests/modules/nf-core/bamtools/split/test.yml b/tests/modules/nf-core/bamtools/split/test.yml index af639b43987..5decdc06e6f 100644 --- a/tests/modules/nf-core/bamtools/split/test.yml +++ b/tests/modules/nf-core/bamtools/split/test.yml @@ -1,5 +1,5 @@ - name: bamtools split test_bamtools_split_single_input - command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/split/nextflow.config tags: - bamtools - bamtools/split @@ -11,7 +11,7 @@ - path: output/bamtools/versions.yml - name: bamtools split test_bamtools_split_multiple - command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/split/nextflow.config tags: - bamtools - bamtools/split diff --git a/tests/modules/nf-core/bamtools/stats/test.yml b/tests/modules/nf-core/bamtools/stats/test.yml index 07811b19793..938a2c7c9ef 100644 --- a/tests/modules/nf-core/bamtools/stats/test.yml +++ b/tests/modules/nf-core/bamtools/stats/test.yml @@ -1,5 +1,5 @@ - name: bamtools stats test_bamtools_stats - command: nextflow run ./tests/modules/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/stats/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/stats/nextflow.config tags: - bamtools/stats - bamtools diff --git a/tests/modules/nf-core/bamutil/trimbam/test.yml b/tests/modules/nf-core/bamutil/trimbam/test.yml index 443a4dedc7e..ec9371afd74 100644 --- a/tests/modules/nf-core/bamutil/trimbam/test.yml +++ b/tests/modules/nf-core/bamutil/trimbam/test.yml @@ -1,5 +1,5 @@ - name: bamutil trimbam test_bamutil_trimbam - command: nextflow run ./tests/modules/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/bamutil/trimbam/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamutil/trimbam/nextflow.config tags: - bamutil/trimbam - bamutil diff --git a/tests/modules/nf-core/bandage/image/test.yml b/tests/modules/nf-core/bandage/image/test.yml index 2abdd175c77..07949fcd17c 100644 --- a/tests/modules/nf-core/bandage/image/test.yml +++ b/tests/modules/nf-core/bandage/image/test.yml @@ -1,5 +1,5 @@ - name: bandage image - command: nextflow run ./tests/modules/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/bandage/image/nextflow.config + command: nextflow run ./tests/modules/nf-core/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bandage/image/nextflow.config tags: - bandage - bandage/image diff --git a/tests/modules/nf-core/bases2fastq/test.yml b/tests/modules/nf-core/bases2fastq/test.yml index bc1245cd487..88fe9c238da 100644 --- a/tests/modules/nf-core/bases2fastq/test.yml +++ b/tests/modules/nf-core/bases2fastq/test.yml @@ -1,5 +1,5 @@ - name: "bases2fastq" - command: nextflow run ./tests/modules/bases2fastq -entry test_bases2fastq -c ./tests/config/nextflow.config -c ./tests/modules/bases2fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/bases2fastq -entry test_bases2fastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bases2fastq/nextflow.config tags: - "bases2fastq" files: diff --git a/tests/modules/nf-core/bbmap/align/test.yml b/tests/modules/nf-core/bbmap/align/test.yml index aa3a9c1c54e..cc3c7f76d3a 100644 --- a/tests/modules/nf-core/bbmap/align/test.yml +++ b/tests/modules/nf-core/bbmap/align/test.yml @@ -1,5 +1,5 @@ - name: bbmap align paired end fasta ref - command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config tags: - bbmap - bbmap/align @@ -9,7 +9,7 @@ - path: output/bbmap/test.bbmap.log - name: bbmap align paired end index ref - command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config tags: - bbmap - bbmap/align @@ -19,7 +19,7 @@ - path: output/bbmap/test.bbmap.log - name: bbmap align single end index ref - command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_single_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config tags: - bbmap - bbmap/align @@ -29,7 +29,7 @@ - path: output/bbmap/test.bbmap.log - name: bbmap align paired end index ref pigz - command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/align/nextflow.config tags: - bbmap - bbmap/align diff --git a/tests/modules/nf-core/bbmap/bbduk/test.yml b/tests/modules/nf-core/bbmap/bbduk/test.yml index 7ab5b9639fc..61543e0042f 100644 --- a/tests/modules/nf-core/bbmap/bbduk/test.yml +++ b/tests/modules/nf-core/bbmap/bbduk/test.yml @@ -1,5 +1,5 @@ - name: bbmap bbduk test_bbmap_bbduk_single_end - command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config tags: - bbmap/bbduk files: @@ -10,7 +10,7 @@ md5sum: a87d0cbd5ced7df8bf1751e4cb407482 - name: bbmap bbduk test_bbmap_bbduk_paired_end - command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config tags: - bbmap/bbduk files: @@ -23,7 +23,7 @@ md5sum: 406e068fbe198f02b48e7e210cc0c69f - name: bbmap bbduk test_bbmap_bbduk_se_ref - command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config tags: - bbmap/bbduk files: @@ -34,7 +34,7 @@ md5sum: 3970e82605c7d109bb348fc94e9eecc0 - name: bbmap bbduk test_bbmap_bbduk_pe_ref - command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbduk/nextflow.config tags: - bbmap/bbduk files: diff --git a/tests/modules/nf-core/bbmap/bbsplit/test.yml b/tests/modules/nf-core/bbmap/bbsplit/test.yml index a1933211848..7c6e4f37d18 100644 --- a/tests/modules/nf-core/bbmap/bbsplit/test.yml +++ b/tests/modules/nf-core/bbmap/bbsplit/test.yml @@ -1,5 +1,5 @@ - name: bbmap bbsplit test_bbmap_bbsplit - command: nextflow run ./tests/modules/bbmap/bbsplit -entry test_bbmap_bbsplit -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbsplit/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/bbsplit -entry test_bbmap_bbsplit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbsplit/nextflow.config tags: - bbmap/bbsplit - bbmap diff --git a/tests/modules/nf-core/bbmap/clumpify/test.yml b/tests/modules/nf-core/bbmap/clumpify/test.yml index 44529ea8801..65975b4f70d 100644 --- a/tests/modules/nf-core/bbmap/clumpify/test.yml +++ b/tests/modules/nf-core/bbmap/clumpify/test.yml @@ -1,5 +1,5 @@ - name: bbmap clumpify test_bbmap_clumpify_single_end - command: nextflow run ./tests/modules/bbmap/clumpify -entry test_bbmap_clumpify_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/clumpify/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config tags: - bbmap/clumpify - bbmap @@ -8,7 +8,7 @@ - path: output/bbmap/test.clumpify.log - name: bbmap clumpify test_bbmap_clumpify_paired_end - command: nextflow run ./tests/modules/bbmap/clumpify -entry test_bbmap_clumpify_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/clumpify/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config tags: - bbmap/clumpify - bbmap diff --git a/tests/modules/nf-core/bbmap/index/test.yml b/tests/modules/nf-core/bbmap/index/test.yml index 4e8d7196b81..d9956fabca4 100644 --- a/tests/modules/nf-core/bbmap/index/test.yml +++ b/tests/modules/nf-core/bbmap/index/test.yml @@ -1,5 +1,5 @@ - name: bbmap index - command: nextflow run ./tests/modules/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/index/nextflow.config tags: - bbmap - bbmap/index diff --git a/tests/modules/nf-core/bbmap/pileup/test.yml b/tests/modules/nf-core/bbmap/pileup/test.yml index 272cdcf79a2..ac65b30a914 100644 --- a/tests/modules/nf-core/bbmap/pileup/test.yml +++ b/tests/modules/nf-core/bbmap/pileup/test.yml @@ -1,5 +1,5 @@ - name: "bbmap pileup" - command: nextflow run ./tests/modules/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/pileup/nextflow.config + command: nextflow run ./tests/modules/nf-core/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/pileup/nextflow.config tags: - "bbmap" - "bbmap/pileup" diff --git a/tests/modules/nf-core/bcftools/annotate/test.yml b/tests/modules/nf-core/bcftools/annotate/test.yml index c3a183b0b3e..34084b50fb0 100644 --- a/tests/modules/nf-core/bcftools/annotate/test.yml +++ b/tests/modules/nf-core/bcftools/annotate/test.yml @@ -1,5 +1,5 @@ - name: bcftools annotate test_bcftools_annotate_out_vcf - command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config tags: - bcftools/annotate - bcftools @@ -9,7 +9,7 @@ md5sum: ff237d88fce62300fdab66b284e9aa95 - name: bcftools annotate test_bcftools_annotate_out_bcf - command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config tags: - bcftools/annotate - bcftools diff --git a/tests/modules/nf-core/bcftools/concat/test.yml b/tests/modules/nf-core/bcftools/concat/test.yml index cffe3d66690..495676f3086 100644 --- a/tests/modules/nf-core/bcftools/concat/test.yml +++ b/tests/modules/nf-core/bcftools/concat/test.yml @@ -1,5 +1,5 @@ - name: bcftools concat test_bcftools_concat_tbi - command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/concat/nextflow.config tags: - bcftools - bcftools/concat @@ -8,7 +8,7 @@ md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df - name: bcftools concat test_bcftools_concat_no_tbi - command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/concat/nextflow.config tags: - bcftools - bcftools/concat diff --git a/tests/modules/nf-core/bcftools/consensus/test.yml b/tests/modules/nf-core/bcftools/consensus/test.yml index 7fa4ecae9e3..26a554217e1 100644 --- a/tests/modules/nf-core/bcftools/consensus/test.yml +++ b/tests/modules/nf-core/bcftools/consensus/test.yml @@ -1,5 +1,5 @@ - name: bcftools consensus test_bcftools_consensus - command: nextflow run ./tests/modules/bcftools/consensus -entry test_bcftools_consensus -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/consensus/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/consensus -entry test_bcftools_consensus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/consensus/nextflow.config tags: - bcftools/consensus - bcftools diff --git a/tests/modules/nf-core/bcftools/convert/test.yml b/tests/modules/nf-core/bcftools/convert/test.yml index 2a031a1b2a9..5d124c5d989 100644 --- a/tests/modules/nf-core/bcftools/convert/test.yml +++ b/tests/modules/nf-core/bcftools/convert/test.yml @@ -1,5 +1,5 @@ - name: bcftools convert test_bcftools_convert_gvcf - command: nextflow run ./tests/modules/bcftools/convert -entry test_bcftools_convert_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/convert/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/convert -entry test_bcftools_convert_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/convert/nextflow.config tags: - bcftools/convert - bcftools @@ -7,7 +7,7 @@ - path: output/bcftools/test.vcf.gz - name: bcftools convert test_bcftools_convert_gvcf_bed - command: nextflow run ./tests/modules/bcftools/convert -entry test_bcftools_convert_gvcf_bed -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/convert/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/convert -entry test_bcftools_convert_gvcf_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/convert/nextflow.config tags: - bcftools/convert - bcftools @@ -15,7 +15,7 @@ - path: output/bcftools/test.vcf.gz - name: bcftools convert test_bcftools_convert_gvcf_to_bcf - command: nextflow run ./tests/modules/bcftools/convert -entry test_bcftools_convert_gvcf_to_bcf -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/convert/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/convert -entry test_bcftools_convert_gvcf_to_bcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/convert/nextflow.config tags: - bcftools/convert - bcftools diff --git a/tests/modules/nf-core/bcftools/filter/test.yml b/tests/modules/nf-core/bcftools/filter/test.yml index 096071bd50e..d877945c9ff 100644 --- a/tests/modules/nf-core/bcftools/filter/test.yml +++ b/tests/modules/nf-core/bcftools/filter/test.yml @@ -1,5 +1,5 @@ - name: bcftools filter test_bcftools_filter - command: nextflow run ./tests/modules/bcftools/filter -entry test_bcftools_filter -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/filter/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/filter -entry test_bcftools_filter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/filter/nextflow.config tags: - bcftools/filter - bcftools diff --git a/tests/modules/nf-core/bcftools/index/test.yml b/tests/modules/nf-core/bcftools/index/test.yml index b8a7d7052ac..6b8112ec08a 100644 --- a/tests/modules/nf-core/bcftools/index/test.yml +++ b/tests/modules/nf-core/bcftools/index/test.yml @@ -1,5 +1,5 @@ - name: bcftools index - command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/index -entry test_bcftools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/index/nextflow.config tags: - bcftools - bcftools/index @@ -8,7 +8,7 @@ md5sum: 9c49464e5983cc02ba89c862c2f33cf8 - name: bcftools index tbi - command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/index -entry test_bcftools_index_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/index/nextflow.config tags: - bcftools - bcftools/index diff --git a/tests/modules/nf-core/bcftools/isec/test.yml b/tests/modules/nf-core/bcftools/isec/test.yml index 6329c34e7fc..9fe3d064e29 100644 --- a/tests/modules/nf-core/bcftools/isec/test.yml +++ b/tests/modules/nf-core/bcftools/isec/test.yml @@ -1,5 +1,5 @@ - name: bcftools isec test_bcftools_isec - command: nextflow run ./tests/modules/bcftools/isec -entry test_bcftools_isec -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/isec/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/isec -entry test_bcftools_isec -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/isec/nextflow.config tags: - bcftools - bcftools/isec diff --git a/tests/modules/nf-core/bcftools/merge/test.yml b/tests/modules/nf-core/bcftools/merge/test.yml index 5bf3be4eb63..edd7eeafee6 100644 --- a/tests/modules/nf-core/bcftools/merge/test.yml +++ b/tests/modules/nf-core/bcftools/merge/test.yml @@ -1,5 +1,5 @@ - name: bcftools merge test_bcftools_merge - command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config tags: - bcftools/merge - bcftools @@ -8,7 +8,7 @@ md5sum: 744b28bef1469aabdcfd354293ef725d - name: bcftools merge test_bcftools_merge_bed - command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge_bed -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config tags: - bcftools/merge - bcftools @@ -17,7 +17,7 @@ md5sum: 9597e71ae1706f76f00707687be43240 - name: bcftools merge test_bcftools_merge_gvcf - command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config tags: - bcftools/merge - bcftools @@ -26,7 +26,7 @@ md5sum: 8aef4d860228cb651e0cb920376f5118 - name: bcftools merge test_bcftools_merge_bcf - command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge_bcf -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/merge -entry test_bcftools_merge_bcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/merge/nextflow.config tags: - bcftools/merge - bcftools diff --git a/tests/modules/nf-core/bcftools/mpileup/test.yml b/tests/modules/nf-core/bcftools/mpileup/test.yml index 85749cdb7c2..d6d0cd6ec2c 100644 --- a/tests/modules/nf-core/bcftools/mpileup/test.yml +++ b/tests/modules/nf-core/bcftools/mpileup/test.yml @@ -1,5 +1,5 @@ - name: bcftools mpileup test_bcftools_mpileup - command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config tags: - bcftools/mpileup - bcftools @@ -12,7 +12,7 @@ md5sum: f37c4bdb0b7a4330477d6716ae2778c2 - name: bcftools mpileup test_bcftools_save_mpileup - command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config tags: - bcftools/mpileup - bcftools diff --git a/tests/modules/nf-core/bcftools/norm/test.yml b/tests/modules/nf-core/bcftools/norm/test.yml index bdc3ce3fdc0..b0d57ec1e9e 100644 --- a/tests/modules/nf-core/bcftools/norm/test.yml +++ b/tests/modules/nf-core/bcftools/norm/test.yml @@ -1,5 +1,5 @@ - name: bcftools norm test_bcftools_norm_no_tbi - command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/norm -entry test_bcftools_norm_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/norm/nextflow.config tags: - bcftools - bcftools/norm @@ -7,7 +7,7 @@ - path: output/bcftools/test2.vcf.gz - name: bcftools norm test_bcftools_norm_tbi - command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/norm -entry test_bcftools_norm_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/norm/nextflow.config tags: - bcftools - bcftools/norm diff --git a/tests/modules/nf-core/bcftools/query/test.yml b/tests/modules/nf-core/bcftools/query/test.yml index 69199109863..829ee630e4d 100644 --- a/tests/modules/nf-core/bcftools/query/test.yml +++ b/tests/modules/nf-core/bcftools/query/test.yml @@ -1,5 +1,5 @@ - name: bcftools query - command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/query/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config tags: - bcftools - bcftools/query @@ -8,7 +8,7 @@ md5sum: c32a6d28f185822d8fe1eeb7e42ec155 - name: bcftools query with optional files - command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/query/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config tags: - bcftools - bcftools/query diff --git a/tests/modules/nf-core/bcftools/reheader/test.yml b/tests/modules/nf-core/bcftools/reheader/test.yml index 2a3e48689fa..84deb70d2c1 100644 --- a/tests/modules/nf-core/bcftools/reheader/test.yml +++ b/tests/modules/nf-core/bcftools/reheader/test.yml @@ -1,5 +1,5 @@ - name: bcftools reheader test_bcftools_reheader_update_sequences - command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/reheader/nextflow.config tags: - bcftools/reheader - bcftools @@ -8,7 +8,7 @@ md5sum: c8a732976911c0c0815d973d5974769a - name: bcftools reheader test_bcftools_reheader_new_header - command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/reheader -entry test_bcftools_reheader_new_header -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/reheader/nextflow.config tags: - bcftools/reheader - bcftools @@ -17,7 +17,7 @@ md5sum: aba91c9ec58e38d73657f02df8457b66 - name: bcftools reheader test_bcftools_reheader_new_header_update_sequences - command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/reheader/nextflow.config tags: - bcftools/reheader - bcftools diff --git a/tests/modules/nf-core/bcftools/roh/test.yml b/tests/modules/nf-core/bcftools/roh/test.yml index 9cc50a6654d..3ea272dd53a 100644 --- a/tests/modules/nf-core/bcftools/roh/test.yml +++ b/tests/modules/nf-core/bcftools/roh/test.yml @@ -1,5 +1,5 @@ - name: "bcftools roh" - command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config tags: - "bcftools" - "bcftools/roh" @@ -8,7 +8,7 @@ - path: "output/bcftools/versions.yml" - name: "bcftools roh stub" - command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config tags: - "bcftools" - "bcftools/roh" diff --git a/tests/modules/nf-core/bcftools/sort/test.yml b/tests/modules/nf-core/bcftools/sort/test.yml index fbb18300ba9..f1e12c54b7d 100644 --- a/tests/modules/nf-core/bcftools/sort/test.yml +++ b/tests/modules/nf-core/bcftools/sort/test.yml @@ -1,5 +1,5 @@ - name: bcftools sort test_bcftools_sort - command: nextflow run tests/modules/bcftools/sort -entry test_bcftools_sort -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/sort -entry test_bcftools_sort -c tests/config/nextflow.config tags: - bcftools - bcftools/sort diff --git a/tests/modules/nf-core/bcftools/stats/test.yml b/tests/modules/nf-core/bcftools/stats/test.yml index 282764463ac..92f3aec93b0 100644 --- a/tests/modules/nf-core/bcftools/stats/test.yml +++ b/tests/modules/nf-core/bcftools/stats/test.yml @@ -1,5 +1,5 @@ - name: bcftools stats test_bcftools_stats - command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/stats/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/stats -entry test_bcftools_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/stats/nextflow.config tags: - bcftools/stats - bcftools @@ -8,7 +8,7 @@ contains: ["TSTV 0 6 2 3.00 6 2 3.00", "DP 0 1 0 0.000000 5 55.555556"] - name: bcftools stats test_bcftools_stats_regions - command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats_regions -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/stats/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/stats -entry test_bcftools_stats_regions -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/stats/nextflow.config tags: - bcftools/stats - bcftools @@ -17,7 +17,7 @@ contains: ["TSTV 0 5 1 5.00 5 1 5.00", "DP 0 1 0 0.000000 3 42.857143"] - name: bcftools stats test_bcftools_stats_targets - command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats_targets -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/stats/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/stats -entry test_bcftools_stats_targets -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/stats/nextflow.config tags: - bcftools/stats - bcftools diff --git a/tests/modules/nf-core/bcftools/view/test.yml b/tests/modules/nf-core/bcftools/view/test.yml index b66402a352c..429a5f56a80 100644 --- a/tests/modules/nf-core/bcftools/view/test.yml +++ b/tests/modules/nf-core/bcftools/view/test.yml @@ -1,5 +1,5 @@ - name: bcftools view - command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/view -entry test_bcftools_view -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/view/nextflow.config tags: - bcftools - bcftools/view @@ -8,7 +8,7 @@ md5sum: c5f2a6a912964c45e8231140420561f9 - name: bcftools view with optional files - command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/view -entry test_bcftools_view_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/view/nextflow.config tags: - bcftools - bcftools/view diff --git a/tests/modules/nf-core/bcl2fastq/test.yml b/tests/modules/nf-core/bcl2fastq/test.yml index 80837fec58a..db222ea8417 100644 --- a/tests/modules/nf-core/bcl2fastq/test.yml +++ b/tests/modules/nf-core/bcl2fastq/test.yml @@ -1,5 +1,5 @@ - name: bcl2fastq test_bcl2fastq - command: nextflow run ./tests/modules/bcl2fastq -entry test_bcl2fastq -c ./tests/config/nextflow.config -c ./tests/modules/bcl2fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcl2fastq -entry test_bcl2fastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcl2fastq/nextflow.config tags: - bcl2fastq files: diff --git a/tests/modules/nf-core/bclconvert/test.yml b/tests/modules/nf-core/bclconvert/test.yml index 1ee3fac5ece..90a557ae046 100644 --- a/tests/modules/nf-core/bclconvert/test.yml +++ b/tests/modules/nf-core/bclconvert/test.yml @@ -1,5 +1,5 @@ - name: bclconvert test_bclconvert - command: nextflow run ./tests/modules/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config -c ./tests/modules/bclconvert/nextflow.config + command: nextflow run ./tests/modules/nf-core/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bclconvert/nextflow.config tags: - bclconvert files: diff --git a/tests/modules/nf-core/bedtools/bamtobed/test.yml b/tests/modules/nf-core/bedtools/bamtobed/test.yml index b038467c7e0..234f5c54f80 100644 --- a/tests/modules/nf-core/bedtools/bamtobed/test.yml +++ b/tests/modules/nf-core/bedtools/bamtobed/test.yml @@ -1,5 +1,5 @@ - name: bedtools bamtobed - command: nextflow run ./tests/modules/bedtools/bamtobed -entry test_bedtools_bamtobed -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/bamtobed/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/bamtobed -entry test_bedtools_bamtobed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/bamtobed/nextflow.config tags: - bedtools - bedtools/bamtobed diff --git a/tests/modules/nf-core/bedtools/complement/test.yml b/tests/modules/nf-core/bedtools/complement/test.yml index 9dbeb36f028..d5cf9b54e4d 100644 --- a/tests/modules/nf-core/bedtools/complement/test.yml +++ b/tests/modules/nf-core/bedtools/complement/test.yml @@ -1,5 +1,5 @@ - name: bedtools complement - command: nextflow run ./tests/modules/bedtools/complement -entry test_bedtools_complement -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/complement/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/complement -entry test_bedtools_complement -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/complement/nextflow.config tags: - bedtools - bedtools/complement diff --git a/tests/modules/nf-core/bedtools/genomecov/test.yml b/tests/modules/nf-core/bedtools/genomecov/test.yml index 8f63bde9cfd..1134218c850 100644 --- a/tests/modules/nf-core/bedtools/genomecov/test.yml +++ b/tests/modules/nf-core/bedtools/genomecov/test.yml @@ -1,5 +1,5 @@ - name: bedtools genomecov test_bedtools_genomecov_noscale - command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config tags: - bedtools - bedtools/genomecov @@ -8,7 +8,7 @@ md5sum: 66083198daca6c001d328ba9616e9b53 - name: bedtools genomecov test_bedtools_genomecov_nonbam_noscale - command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config tags: - bedtools - bedtools/genomecov @@ -17,7 +17,7 @@ md5sum: f47b58840087426e5b643d8dfd155c1f - name: bedtools genomecov test_bedtools_genomecov_scale - command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_scale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_scale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config tags: - bedtools - bedtools/genomecov @@ -26,7 +26,7 @@ md5sum: 01291b6e1beab72e046653e709eb0e10 - name: bedtools genomecov test_bedtools_genomecov_nonbam_scale - command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/genomecov/nextflow.config tags: - bedtools - bedtools/genomecov diff --git a/tests/modules/nf-core/bedtools/getfasta/test.yml b/tests/modules/nf-core/bedtools/getfasta/test.yml index a455f861099..8b9f309d02d 100644 --- a/tests/modules/nf-core/bedtools/getfasta/test.yml +++ b/tests/modules/nf-core/bedtools/getfasta/test.yml @@ -1,5 +1,5 @@ - name: bedtools getfasta - command: nextflow run ./tests/modules/bedtools/getfasta -entry test_bedtools_getfasta -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/getfasta/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/getfasta -entry test_bedtools_getfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/getfasta/nextflow.config tags: - bedtools - bedtools/getfasta diff --git a/tests/modules/nf-core/bedtools/intersect/test.yml b/tests/modules/nf-core/bedtools/intersect/test.yml index 86fe70cde03..fc96a00b71e 100644 --- a/tests/modules/nf-core/bedtools/intersect/test.yml +++ b/tests/modules/nf-core/bedtools/intersect/test.yml @@ -1,5 +1,5 @@ - name: bedtools intersect test_bedtools_intersect - command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/intersect/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/intersect -entry test_bedtools_intersect -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/intersect/nextflow.config tags: - bedtools - bedtools/intersect @@ -8,7 +8,7 @@ md5sum: afcbf01c2f2013aad71dbe8e34f2c15c - name: bedtools intersect test_bedtools_intersect_bam - command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect_bam -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/intersect/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/intersect -entry test_bedtools_intersect_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/intersect/nextflow.config tags: - bedtools - bedtools/intersect diff --git a/tests/modules/nf-core/bedtools/makewindows/test.yml b/tests/modules/nf-core/bedtools/makewindows/test.yml index 8accaa3613c..3fa43b342a1 100644 --- a/tests/modules/nf-core/bedtools/makewindows/test.yml +++ b/tests/modules/nf-core/bedtools/makewindows/test.yml @@ -1,5 +1,5 @@ - name: bedtools makewindows test_bedtools_makewindows - command: nextflow run ./tests/modules/bedtools/makewindows -entry test_bedtools_makewindows -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/makewindows/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config tags: - bedtools/makewindows - bedtools diff --git a/tests/modules/nf-core/bedtools/maskfasta/test.yml b/tests/modules/nf-core/bedtools/maskfasta/test.yml index f1e8f35a9ea..62c834a8c09 100644 --- a/tests/modules/nf-core/bedtools/maskfasta/test.yml +++ b/tests/modules/nf-core/bedtools/maskfasta/test.yml @@ -1,5 +1,5 @@ - name: bedtools maskfasta - command: nextflow run ./tests/modules/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/maskfasta/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/maskfasta/nextflow.config tags: - bedtools - bedtools/maskfasta diff --git a/tests/modules/nf-core/bedtools/merge/test.yml b/tests/modules/nf-core/bedtools/merge/test.yml index 5fc8b0344a8..bee9b75ba5f 100644 --- a/tests/modules/nf-core/bedtools/merge/test.yml +++ b/tests/modules/nf-core/bedtools/merge/test.yml @@ -1,5 +1,5 @@ - name: bedtools merge - command: nextflow run ./tests/modules/bedtools/merge -entry test_bedtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/merge -entry test_bedtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/merge/nextflow.config tags: - bedtools - bedtools/merge diff --git a/tests/modules/nf-core/bedtools/slop/test.yml b/tests/modules/nf-core/bedtools/slop/test.yml index 0d49e66b775..a69dedb6317 100644 --- a/tests/modules/nf-core/bedtools/slop/test.yml +++ b/tests/modules/nf-core/bedtools/slop/test.yml @@ -1,5 +1,5 @@ - name: bedtools slop - command: nextflow run ./tests/modules/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/slop/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/slop/nextflow.config tags: - bedtools - bedtools/slop diff --git a/tests/modules/nf-core/bedtools/sort/test.yml b/tests/modules/nf-core/bedtools/sort/test.yml index 173f0587aa5..64336a88af2 100644 --- a/tests/modules/nf-core/bedtools/sort/test.yml +++ b/tests/modules/nf-core/bedtools/sort/test.yml @@ -1,5 +1,5 @@ - name: bedtools sort - command: nextflow run ./tests/modules/bedtools/sort -entry test_bedtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/sort/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/sort -entry test_bedtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/sort/nextflow.config tags: - bedtools - bedtools/sort diff --git a/tests/modules/nf-core/bedtools/split/test.yml b/tests/modules/nf-core/bedtools/split/test.yml index 92ac17fa318..330069c25aa 100644 --- a/tests/modules/nf-core/bedtools/split/test.yml +++ b/tests/modules/nf-core/bedtools/split/test.yml @@ -1,5 +1,5 @@ - name: bedtools split test_bedtools_split - command: nextflow run ./tests/modules/bedtools/split -entry test_bedtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/split/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/split -entry test_bedtools_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/split/nextflow.config tags: - bedtools - bedtools/split diff --git a/tests/modules/nf-core/bedtools/subtract/test.yml b/tests/modules/nf-core/bedtools/subtract/test.yml index 52b57436571..efb1863cbaa 100644 --- a/tests/modules/nf-core/bedtools/subtract/test.yml +++ b/tests/modules/nf-core/bedtools/subtract/test.yml @@ -1,5 +1,5 @@ - name: bedtools subtract - command: nextflow run ./tests/modules/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/subtract/nextflow.config + command: nextflow run ./tests/modules/nf-core/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/subtract/nextflow.config tags: - bedtools - bedtools/subtract diff --git a/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml b/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml index 7c16fcf1911..3e280b383ab 100644 --- a/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml +++ b/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml @@ -1,5 +1,5 @@ - name: biobambam bammarkduplicates2 test_biobambam_bammarkduplicates2 - command: nextflow run tests/modules/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c tests/config/nextflow.config tags: - biobambam/bammarkduplicates2 - biobambam diff --git a/tests/modules/nf-core/biobambam/bammerge/test.yml b/tests/modules/nf-core/biobambam/bammerge/test.yml index d68b70834a1..c886635b878 100644 --- a/tests/modules/nf-core/biobambam/bammerge/test.yml +++ b/tests/modules/nf-core/biobambam/bammerge/test.yml @@ -1,5 +1,5 @@ - name: biobambam bammerge test_biobambam_bammerge_paired - command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_paired -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bammerge/nextflow.config + command: nextflow run ./tests/modules/nf-core/biobambam/bammerge -entry test_biobambam_bammerge_paired -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/biobambam/bammerge/nextflow.config tags: - biobambam/bammerge - biobambam @@ -12,7 +12,7 @@ md5sum: 31c59857990ceb392242136429e30243 - name: biobambam bammerge test_biobambam_bammerge_single - command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bammerge/nextflow.config + command: nextflow run ./tests/modules/nf-core/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/biobambam/bammerge/nextflow.config tags: - biobambam/bammerge - biobambam diff --git a/tests/modules/nf-core/biobambam/bamsormadup/test.yml b/tests/modules/nf-core/biobambam/bamsormadup/test.yml index d197038ee86..4837c16f042 100644 --- a/tests/modules/nf-core/biobambam/bamsormadup/test.yml +++ b/tests/modules/nf-core/biobambam/bamsormadup/test.yml @@ -1,5 +1,5 @@ - name: biobambam bamsormadup test_biobambam_bamsormadup_multi_input - command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config + command: nextflow run ./tests/modules/nf-core/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/biobambam/bamsormadup/nextflow.config tags: - biobambam - biobambam/bamsormadup @@ -10,7 +10,7 @@ md5sum: 1721879bea1f3888ecd33b35e6ee0e72 - name: biobambam bamsormadup test_biobambam_bamsormadup_single_input - command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config + command: nextflow run ./tests/modules/nf-core/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/biobambam/bamsormadup/nextflow.config tags: - biobambam - biobambam/bamsormadup diff --git a/tests/modules/nf-core/biscuit/align/test.yml b/tests/modules/nf-core/biscuit/align/test.yml index bf778ff55ae..fff02b26a24 100644 --- a/tests/modules/nf-core/biscuit/align/test.yml +++ b/tests/modules/nf-core/biscuit/align/test.yml @@ -1,5 +1,5 @@ - name: biscuit align test_biscuit_align_single - command: nextflow run tests/modules/biscuit/align -entry test_biscuit_align_single -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_single -c tests/config/nextflow.config tags: - biscuit - biscuit/align @@ -26,7 +26,7 @@ md5sum: a86c4170bbf90cc75b93eb59ea124acd - name: biscuit align test_biscuit_align_paired - command: nextflow run tests/modules/biscuit/align -entry test_biscuit_align_paired -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_paired -c tests/config/nextflow.config tags: - biscuit - biscuit/align diff --git a/tests/modules/nf-core/biscuit/biscuitblaster/test.yml b/tests/modules/nf-core/biscuit/biscuitblaster/test.yml index 37bb654360b..03b44837bf6 100644 --- a/tests/modules/nf-core/biscuit/biscuitblaster/test.yml +++ b/tests/modules/nf-core/biscuit/biscuitblaster/test.yml @@ -1,5 +1,5 @@ - name: biscuit biscuitblaster test_biscuit_blaster_single - command: nextflow run tests/modules/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c tests/config/nextflow.config tags: - biscuit/biscuitblaster - biscuit @@ -28,7 +28,7 @@ md5sum: bfb660b5b0d92dde6817a1c6a2a302bb - name: biscuit biscuitblaster test_biscuit_blaster_paired - command: nextflow run tests/modules/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c tests/config/nextflow.config tags: - biscuit/biscuitblaster - biscuit diff --git a/tests/modules/nf-core/biscuit/bsconv/test.yml b/tests/modules/nf-core/biscuit/bsconv/test.yml index 528a4fe5edd..737f3d1ae80 100644 --- a/tests/modules/nf-core/biscuit/bsconv/test.yml +++ b/tests/modules/nf-core/biscuit/bsconv/test.yml @@ -1,5 +1,5 @@ - name: biscuit bsconv test_biscuit_bsconv - command: nextflow run tests/modules/biscuit/bsconv -entry test_biscuit_bsconv -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/bsconv -entry test_biscuit_bsconv -c tests/config/nextflow.config tags: - biscuit - biscuit/bsconv diff --git a/tests/modules/nf-core/biscuit/epiread/test.yml b/tests/modules/nf-core/biscuit/epiread/test.yml index 1db86982a85..7cd1fe9d210 100644 --- a/tests/modules/nf-core/biscuit/epiread/test.yml +++ b/tests/modules/nf-core/biscuit/epiread/test.yml @@ -1,5 +1,5 @@ - name: biscuit epiread test_biscuit_epiread_nosnp - command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_nosnp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_nosnp -c tests/config/nextflow.config tags: - biscuit - biscuit/epiread @@ -26,7 +26,7 @@ md5sum: 674a77ac5ca8f4b42d30e58e30c3a9af - name: biscuit epiread test_biscuit_epiread_snp - command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp -c tests/config/nextflow.config tags: - biscuit - biscuit/epiread @@ -53,7 +53,7 @@ md5sum: f2f7c4ff3c6a135b1c8a3aff24a44d81 - name: biscuit epiread test_biscuit_epiread_snp_decompress - command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c tests/config/nextflow.config tags: - biscuit - biscuit/epiread diff --git a/tests/modules/nf-core/biscuit/index/test.yml b/tests/modules/nf-core/biscuit/index/test.yml index a2e4cb67f78..73fdde94d6f 100644 --- a/tests/modules/nf-core/biscuit/index/test.yml +++ b/tests/modules/nf-core/biscuit/index/test.yml @@ -1,5 +1,5 @@ - name: biscuit index test_biscuit_index - command: nextflow run tests/modules/biscuit/index -entry test_biscuit_index -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/index -entry test_biscuit_index -c tests/config/nextflow.config tags: - biscuit/index - biscuit diff --git a/tests/modules/nf-core/biscuit/mergecg/test.yml b/tests/modules/nf-core/biscuit/mergecg/test.yml index 7b2408bb95d..2aca1b25176 100644 --- a/tests/modules/nf-core/biscuit/mergecg/test.yml +++ b/tests/modules/nf-core/biscuit/mergecg/test.yml @@ -1,5 +1,5 @@ - name: biscuit mergecg test_biscuit_mergecg - command: nextflow run tests/modules/biscuit/mergecg -entry test_biscuit_mergecg -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/mergecg -entry test_biscuit_mergecg -c tests/config/nextflow.config tags: - biscuit - biscuit/mergecg diff --git a/tests/modules/nf-core/biscuit/pileup/test.yml b/tests/modules/nf-core/biscuit/pileup/test.yml index ad840737b9e..dd02371dd7c 100644 --- a/tests/modules/nf-core/biscuit/pileup/test.yml +++ b/tests/modules/nf-core/biscuit/pileup/test.yml @@ -1,5 +1,5 @@ - name: biscuit pileup test_biscuit_pileup - command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup -c tests/config/nextflow.config tags: - biscuit - biscuit/pileup @@ -26,7 +26,7 @@ md5sum: ae38b891fdbf9f7ff5c486408f949dc5 - name: biscuit pileup test_biscuit_pileup_somatic - command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup_somatic -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup_somatic -c tests/config/nextflow.config tags: - biscuit - biscuit/pileup diff --git a/tests/modules/nf-core/biscuit/qc/test.yml b/tests/modules/nf-core/biscuit/qc/test.yml index ed33dd30255..4655e39c3c0 100644 --- a/tests/modules/nf-core/biscuit/qc/test.yml +++ b/tests/modules/nf-core/biscuit/qc/test.yml @@ -1,5 +1,5 @@ - name: biscuit qc test_biscuit_qc - command: nextflow run tests/modules/biscuit/qc -entry test_biscuit_qc -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/qc -entry test_biscuit_qc -c tests/config/nextflow.config tags: - biscuit/qc - biscuit diff --git a/tests/modules/nf-core/biscuit/vcf2bed/test.yml b/tests/modules/nf-core/biscuit/vcf2bed/test.yml index 7eaa29727c0..ee00d493171 100644 --- a/tests/modules/nf-core/biscuit/vcf2bed/test.yml +++ b/tests/modules/nf-core/biscuit/vcf2bed/test.yml @@ -1,5 +1,5 @@ - name: biscuit vcf2bed test_biscuit_vcf2bed - command: nextflow run tests/modules/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config tags: - biscuit/vcf2bed - biscuit diff --git a/tests/modules/nf-core/bismark/align/test.yml b/tests/modules/nf-core/bismark/align/test.yml index ffae05afc22..a7362eb0d2a 100644 --- a/tests/modules/nf-core/bismark/align/test.yml +++ b/tests/modules/nf-core/bismark/align/test.yml @@ -1,5 +1,5 @@ - name: bismark align single-end test workflow - command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bismark/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/align -entry test_bismark_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/align/nextflow.config tags: - bismark - bismark/align @@ -9,7 +9,7 @@ - path: output/bismark/test.methylated_1_bismark_bt2_SE_report.txt - name: bismark align paired-end test workflow - command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bismark/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/align -entry test_bismark_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/align/nextflow.config tags: - bismark - bismark/align diff --git a/tests/modules/nf-core/bismark/deduplicate/test.yml b/tests/modules/nf-core/bismark/deduplicate/test.yml index 12099750195..ba4d2de7a3d 100644 --- a/tests/modules/nf-core/bismark/deduplicate/test.yml +++ b/tests/modules/nf-core/bismark/deduplicate/test.yml @@ -1,5 +1,5 @@ - name: bismark deduplicate test workflow - command: nextflow run ./tests/modules/bismark/deduplicate -entry test_bismark_deduplicate -c ./tests/config/nextflow.config -c ./tests/modules/bismark/deduplicate/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/deduplicate -entry test_bismark_deduplicate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/deduplicate/nextflow.config tags: - bismark - bismark/deduplicate diff --git a/tests/modules/nf-core/bismark/genomepreparation/test.yml b/tests/modules/nf-core/bismark/genomepreparation/test.yml index a0d3c0724ae..8868eed3de5 100644 --- a/tests/modules/nf-core/bismark/genomepreparation/test.yml +++ b/tests/modules/nf-core/bismark/genomepreparation/test.yml @@ -1,5 +1,5 @@ - name: bismark genomepreparation test workflow - command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c ./tests/config/nextflow.config -c ./tests/modules/bismark/genomepreparation/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/genomepreparation -entry test_bismark_genomepreparation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/genomepreparation/nextflow.config tags: - bismark - bismark/genomepreparation diff --git a/tests/modules/nf-core/bismark/methylationextractor/test.yml b/tests/modules/nf-core/bismark/methylationextractor/test.yml index f25b7646957..ef1643dfff6 100644 --- a/tests/modules/nf-core/bismark/methylationextractor/test.yml +++ b/tests/modules/nf-core/bismark/methylationextractor/test.yml @@ -1,5 +1,5 @@ - name: bismark methylation extractor test workflow - command: nextflow run ./tests/modules/bismark/methylationextractor -entry test_bismark_methylationextractor -c ./tests/config/nextflow.config -c ./tests/modules/bismark/methylationextractor/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/methylationextractor -entry test_bismark_methylationextractor -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/methylationextractor/nextflow.config tags: - bismark - bismark/methylationextractor diff --git a/tests/modules/nf-core/bismark/report/test.yml b/tests/modules/nf-core/bismark/report/test.yml index 9195994cbcc..591d2789a2e 100644 --- a/tests/modules/nf-core/bismark/report/test.yml +++ b/tests/modules/nf-core/bismark/report/test.yml @@ -1,5 +1,5 @@ - name: bismark report test workflow - command: nextflow run ./tests/modules/bismark/report -entry test_bismark_report -c ./tests/config/nextflow.config -c ./tests/modules/bismark/report/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/report -entry test_bismark_report -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/report/nextflow.config tags: - bismark - bismark/report diff --git a/tests/modules/nf-core/bismark/summary/test.yml b/tests/modules/nf-core/bismark/summary/test.yml index 3b5196b919b..d4ccddaadaf 100644 --- a/tests/modules/nf-core/bismark/summary/test.yml +++ b/tests/modules/nf-core/bismark/summary/test.yml @@ -1,5 +1,5 @@ - name: bismark summary test workflow - command: nextflow run ./tests/modules/bismark/summary -entry test_bismark_summary -c ./tests/config/nextflow.config -c ./tests/modules/bismark/summary/nextflow.config + command: nextflow run ./tests/modules/nf-core/bismark/summary -entry test_bismark_summary -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bismark/summary/nextflow.config tags: - bismark - bismark/summary diff --git a/tests/modules/nf-core/blast/blastn/test.yml b/tests/modules/nf-core/blast/blastn/test.yml index 17522c9b822..2c3492a1b07 100644 --- a/tests/modules/nf-core/blast/blastn/test.yml +++ b/tests/modules/nf-core/blast/blastn/test.yml @@ -1,5 +1,5 @@ - name: blast_blastn - command: nextflow run ./tests/modules/blast/blastn -entry test_blast_blastn -c ./tests/config/nextflow.config -c ./tests/modules/blast/blastn/nextflow.config + command: nextflow run ./tests/modules/nf-core/blast/blastn -entry test_blast_blastn -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blast/blastn/nextflow.config tags: - blast - blast/blastn diff --git a/tests/modules/nf-core/blast/makeblastdb/test.yml b/tests/modules/nf-core/blast/makeblastdb/test.yml index 3b59f3f67db..a1f527fb430 100644 --- a/tests/modules/nf-core/blast/makeblastdb/test.yml +++ b/tests/modules/nf-core/blast/makeblastdb/test.yml @@ -1,5 +1,5 @@ - name: blast_makeblastdb - command: nextflow run ./tests/modules/blast/makeblastdb -entry test_blast_makeblastdb -c ./tests/config/nextflow.config -c ./tests/modules/blast/makeblastdb/nextflow.config + command: nextflow run ./tests/modules/nf-core/blast/makeblastdb -entry test_blast_makeblastdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blast/makeblastdb/nextflow.config tags: - blast - blast/makeblastdb diff --git a/tests/modules/nf-core/blast/tblastn/test.yml b/tests/modules/nf-core/blast/tblastn/test.yml index b545edbe2c7..89887a007b8 100644 --- a/tests/modules/nf-core/blast/tblastn/test.yml +++ b/tests/modules/nf-core/blast/tblastn/test.yml @@ -1,5 +1,5 @@ - name: blast tblastn - command: nextflow run ./tests/modules/blast/tblastn -entry test_blast_tblastn -c ./tests/config/nextflow.config -c ./tests/modules/blast/tblastn/nextflow.config + command: nextflow run ./tests/modules/nf-core/blast/tblastn -entry test_blast_tblastn -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blast/tblastn/nextflow.config tags: - blast - blast/tblastn diff --git a/tests/modules/nf-core/bowtie/align/test.yml b/tests/modules/nf-core/bowtie/align/test.yml index 1f8d1294b3d..45ebb7598f7 100644 --- a/tests/modules/nf-core/bowtie/align/test.yml +++ b/tests/modules/nf-core/bowtie/align/test.yml @@ -1,5 +1,5 @@ - name: bowtie align single-end - command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie/align/nextflow.config tags: - bowtie - bowtie/align @@ -21,7 +21,7 @@ md5sum: d9b76ecf9fd0413240173273b38d8199 - name: bowtie align paired-end - command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie/align/nextflow.config tags: - bowtie - bowtie/align diff --git a/tests/modules/nf-core/bowtie/build_test/test.yml b/tests/modules/nf-core/bowtie/build_test/test.yml index c51d1e8a362..04a48375e3c 100644 --- a/tests/modules/nf-core/bowtie/build_test/test.yml +++ b/tests/modules/nf-core/bowtie/build_test/test.yml @@ -1,5 +1,5 @@ - name: bowtie build - command: nextflow run ./tests/modules/bowtie/build_test -entry test_bowtie_build -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/build/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie/build_test -entry test_bowtie_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie/build/nextflow.config tags: - bowtie - bowtie/build diff --git a/tests/modules/nf-core/bowtie2/align/test.yml b/tests/modules/nf-core/bowtie2/align/test.yml index 9c9ff7a1a6f..f9944d60897 100644 --- a/tests/modules/nf-core/bowtie2/align/test.yml +++ b/tests/modules/nf-core/bowtie2/align/test.yml @@ -1,5 +1,5 @@ - name: bowtie2 align test_bowtie2_align_single_end - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config tags: - bowtie2 - bowtie2/align @@ -9,7 +9,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_single_end_sorted - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config tags: - bowtie2 - bowtie2/align @@ -19,7 +19,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_paired_end - command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config tags: - bowtie2 - bowtie2/align @@ -29,7 +29,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_single_end_large_index - command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index tags: - bowtie2 - bowtie2/align @@ -39,7 +39,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_paired_end_large_index - command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index tags: - bowtie2 - bowtie2/align diff --git a/tests/modules/nf-core/bowtie2/build_test/test.yml b/tests/modules/nf-core/bowtie2/build_test/test.yml index 88e6c3ada1d..fe5817e2642 100644 --- a/tests/modules/nf-core/bowtie2/build_test/test.yml +++ b/tests/modules/nf-core/bowtie2/build_test/test.yml @@ -1,5 +1,5 @@ - name: bowtie2 build - command: nextflow run ./tests/modules/bowtie2/build_test -entry test_bowtie2_build -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/build/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie2/build_test -entry test_bowtie2_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/build/nextflow.config tags: - bowtie2 - bowtie2/build diff --git a/tests/modules/nf-core/bracken/bracken/test.yml b/tests/modules/nf-core/bracken/bracken/test.yml index 373314f7ea9..cb64523d770 100644 --- a/tests/modules/nf-core/bracken/bracken/test.yml +++ b/tests/modules/nf-core/bracken/bracken/test.yml @@ -1,5 +1,5 @@ - name: bracken bracken test_bracken_bracken_single_end_default_args - command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c tests/config/nextflow.config tags: - bracken/bracken - bracken @@ -10,7 +10,7 @@ md5sum: e0abdac999c0d58becd8c868dd12028b - name: bracken bracken test_bracken_bracken_single_end_custom_args - command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config tags: - bracken/bracken - bracken @@ -21,7 +21,7 @@ md5sum: 7d0a1629ece197a8062271d39ed8ef74 - name: bracken bracken test_bracken_bracken_paired_end_default_args - command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config tags: - bracken/bracken - bracken @@ -32,7 +32,7 @@ md5sum: 7b58898d0b9cce1ca170ac5a82d8ecf1 - name: bracken bracken test_bracken_bracken_paired_end_custom_args - command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config tags: - bracken/bracken - bracken diff --git a/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml b/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml index 057a215f32a..ebf64da70e2 100644 --- a/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml +++ b/tests/modules/nf-core/bracken/combinebrackenoutputs/test.yml @@ -1,5 +1,5 @@ - name: bracken combinebrackenoutputs test_bracken_combinebrackenoutputs - command: nextflow run ./tests/modules/bracken/combinebrackenoutputs -entry test_bracken_combinebrackenoutputs -c ./tests/config/nextflow.config -c ./tests/modules/bracken/combinebrackenoutputs/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/combinebrackenoutputs -entry test_bracken_combinebrackenoutputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bracken/combinebrackenoutputs/nextflow.config tags: - bracken/combinebrackenoutputs - bracken diff --git a/tests/modules/nf-core/busco/test.yml b/tests/modules/nf-core/busco/test.yml index 562f427fa8d..caaaba1b182 100644 --- a/tests/modules/nf-core/busco/test.yml +++ b/tests/modules/nf-core/busco/test.yml @@ -1,5 +1,5 @@ - name: busco test_busco_genome_single_fasta - command: nextflow run ./tests/modules/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config + command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/busco/nextflow.config tags: - busco files: @@ -82,7 +82,7 @@ - "how to cite BUSCO" - name: busco test_busco_genome_multi_fasta - command: nextflow run ./tests/modules/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config + command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/busco/nextflow.config tags: - busco files: @@ -247,7 +247,7 @@ - "how to cite BUSCO" - name: busco test_busco_eukaryote_metaeuk - command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config + command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/busco/nextflow.config tags: - busco files: @@ -324,7 +324,7 @@ - "how to cite BUSCO" - name: busco test_busco_eukaryote_augustus - command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config + command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/busco/nextflow.config tags: - busco files: @@ -384,7 +384,7 @@ - "Running Augustus gene predictor" - name: busco test_busco_protein - command: nextflow run ./tests/modules/busco -entry test_busco_protein -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config + command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_protein -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/busco/nextflow.config tags: - busco files: @@ -435,7 +435,7 @@ - "busco:" - name: busco test_busco_transcriptome - command: nextflow run ./tests/modules/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config + command: nextflow run ./tests/modules/nf-core/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/busco/nextflow.config tags: - busco files: diff --git a/tests/modules/nf-core/bwa/aln/test.yml b/tests/modules/nf-core/bwa/aln/test.yml index c89c47be844..8a3bec17ae2 100644 --- a/tests/modules/nf-core/bwa/aln/test.yml +++ b/tests/modules/nf-core/bwa/aln/test.yml @@ -1,5 +1,5 @@ - name: bwa aln single-end - command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/aln/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/aln -entry test_bwa_aln_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/aln/nextflow.config tags: - bwa - bwa/aln @@ -18,7 +18,7 @@ md5sum: ab3952cabf026b48cd3eb5bccbb636d1 - name: bwa aln paired-end - command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/aln/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/aln -entry test_bwa_aln_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/aln/nextflow.config tags: - bwa - bwa/aln diff --git a/tests/modules/nf-core/bwa/index/test.yml b/tests/modules/nf-core/bwa/index/test.yml index a9dab91d632..7d313195fad 100644 --- a/tests/modules/nf-core/bwa/index/test.yml +++ b/tests/modules/nf-core/bwa/index/test.yml @@ -1,5 +1,5 @@ - name: bwa index test_bwa_index - command: nextflow run ./tests/modules/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/bwa/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/index/nextflow.config tags: - bwa - bwa/index diff --git a/tests/modules/nf-core/bwa/mem/test.yml b/tests/modules/nf-core/bwa/mem/test.yml index 8fe2ee6b015..7e8157b8bec 100644 --- a/tests/modules/nf-core/bwa/mem/test.yml +++ b/tests/modules/nf-core/bwa/mem/test.yml @@ -1,5 +1,5 @@ - name: bwa mem single-end - command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config tags: - bwa - bwa/mem @@ -17,7 +17,7 @@ md5sum: ab3952cabf026b48cd3eb5bccbb636d1 - name: bwa mem single-end sort - command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config tags: - bwa - bwa/mem @@ -35,7 +35,7 @@ md5sum: ab3952cabf026b48cd3eb5bccbb636d1 - name: bwa mem paired-end - command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config tags: - bwa - bwa/mem @@ -53,7 +53,7 @@ md5sum: ab3952cabf026b48cd3eb5bccbb636d1 - name: bwa mem paired-end sort - command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config tags: - bwa - bwa/mem diff --git a/tests/modules/nf-core/bwa/sampe/test.yml b/tests/modules/nf-core/bwa/sampe/test.yml index c3eb42f8789..1fbc1f9fb1f 100644 --- a/tests/modules/nf-core/bwa/sampe/test.yml +++ b/tests/modules/nf-core/bwa/sampe/test.yml @@ -1,5 +1,5 @@ - name: bwa sampe - command: nextflow run ./tests/modules/bwa/sampe -entry test_bwa_sampe -c ./tests/config/nextflow.config -c ./tests/modules/bwa/sampe/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/sampe -entry test_bwa_sampe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/sampe/nextflow.config tags: - bwa - bwa/sampe diff --git a/tests/modules/nf-core/bwa/samse/test.yml b/tests/modules/nf-core/bwa/samse/test.yml index 3af39258e0d..db3a8bf2450 100644 --- a/tests/modules/nf-core/bwa/samse/test.yml +++ b/tests/modules/nf-core/bwa/samse/test.yml @@ -1,5 +1,5 @@ - name: bwa samse - command: nextflow run ./tests/modules/bwa/samse -entry test_bwa_samse -c ./tests/config/nextflow.config -c ./tests/modules/bwa/samse/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwa/samse -entry test_bwa_samse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/samse/nextflow.config tags: - bwa - bwa/samse diff --git a/tests/modules/nf-core/bwamem2/index/test.yml b/tests/modules/nf-core/bwamem2/index/test.yml index efada6ec54f..be000b25857 100644 --- a/tests/modules/nf-core/bwamem2/index/test.yml +++ b/tests/modules/nf-core/bwamem2/index/test.yml @@ -1,5 +1,5 @@ - name: bwamem2 index - command: nextflow run ./tests/modules/bwamem2/index -entry test_bwamem2_index -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwamem2/index -entry test_bwamem2_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/index/nextflow.config tags: - bwamem2 - bwamem2/index diff --git a/tests/modules/nf-core/bwamem2/mem/test.yml b/tests/modules/nf-core/bwamem2/mem/test.yml index bf445ebeeeb..d693fc72840 100644 --- a/tests/modules/nf-core/bwamem2/mem/test.yml +++ b/tests/modules/nf-core/bwamem2/mem/test.yml @@ -1,5 +1,5 @@ - name: bwamem2 mem single-end - command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config tags: - bwamem2 - bwamem2/mem @@ -17,7 +17,7 @@ md5sum: c32e11f6c859f166c7525a9c1d583567 - name: bwamem2 mem single-end sort - command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config tags: - bwamem2 - bwamem2/mem @@ -35,7 +35,7 @@ md5sum: c32e11f6c859f166c7525a9c1d583567 - name: bwamem2 mem paired-end - command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config tags: - bwamem2 - bwamem2/mem @@ -53,7 +53,7 @@ md5sum: c32e11f6c859f166c7525a9c1d583567 - name: bwamem2 mem paired-end sort - command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwamem2/mem -entry test_bwamem2_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwamem2/mem/nextflow.config tags: - bwamem2 - bwamem2/mem diff --git a/tests/modules/nf-core/bwameth/align/test.yml b/tests/modules/nf-core/bwameth/align/test.yml index 161c627f7c1..6474091306e 100644 --- a/tests/modules/nf-core/bwameth/align/test.yml +++ b/tests/modules/nf-core/bwameth/align/test.yml @@ -1,5 +1,5 @@ - name: bwameth align single-end test workflow - command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwameth/align -entry test_bwameth_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwameth/align/nextflow.config tags: - bwameth - bwameth/align @@ -7,7 +7,7 @@ - path: output/bwameth/test.bam - name: bwameth align paired-end test workflow - command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwameth/align -entry test_bwameth_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwameth/align/nextflow.config tags: - bwameth - bwameth/align diff --git a/tests/modules/nf-core/bwameth/index/test.yml b/tests/modules/nf-core/bwameth/index/test.yml index 9783c511e60..9d35893640c 100644 --- a/tests/modules/nf-core/bwameth/index/test.yml +++ b/tests/modules/nf-core/bwameth/index/test.yml @@ -1,5 +1,5 @@ - name: bwameth index test workflow - command: nextflow run ./tests/modules/bwameth/index -entry test_bwameth_index -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/bwameth/index -entry test_bwameth_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwameth/index/nextflow.config tags: - bwameth - bwameth/index diff --git a/tests/modules/nf-core/cat/cat/test.yml b/tests/modules/nf-core/cat/cat/test.yml index 9710b6659ae..6c2b7aa5061 100644 --- a/tests/modules/nf-core/cat/cat/test.yml +++ b/tests/modules/nf-core/cat/cat/test.yml @@ -1,5 +1,5 @@ - name: cat unzipped unzipped - command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config tags: - cat - cat/cat @@ -8,7 +8,7 @@ md5sum: f44b33a0e441ad58b2d3700270e2dbe2 - name: cat unzipped unzipped stub - command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run tags: - cat - cat/cat @@ -16,7 +16,7 @@ - path: output/cat/test.fasta - name: cat zipped zipped - command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config tags: - cat - cat/cat @@ -24,7 +24,7 @@ - path: output/cat/test.gz - name: cat zipped zipped stub - command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run tags: - cat - cat/cat @@ -32,7 +32,7 @@ - path: output/cat/test.gz - name: cat zipped unzipped - command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config tags: - cat - cat/cat @@ -41,7 +41,7 @@ md5sum: c439d3b60e7bc03e8802a451a0d9a5d9 - name: cat zipped unzipped stub - command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run tags: - cat - cat/cat @@ -49,7 +49,7 @@ - path: output/cat/cat.txt - name: cat unzipped zipped - command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config tags: - cat - cat/cat @@ -57,7 +57,7 @@ - path: output/cat/cat.txt.gz - name: cat unzipped zipped stub - command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run tags: - cat - cat/cat @@ -65,7 +65,7 @@ - path: output/cat/cat.txt.gz - name: cat one file unzipped zipped - command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config tags: - cat - cat/cat @@ -73,7 +73,7 @@ - path: output/cat/cat.txt.gz - name: cat one file unzipped zipped stub - command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/cat/nextflow.config -stub-run tags: - cat - cat/cat diff --git a/tests/modules/nf-core/cat/fastq/test.yml b/tests/modules/nf-core/cat/fastq/test.yml index 416f1a8b449..51085494010 100644 --- a/tests/modules/nf-core/cat/fastq/test.yml +++ b/tests/modules/nf-core/cat/fastq/test.yml @@ -1,5 +1,5 @@ - name: cat fastq single-end - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config tags: - cat - cat/fastq @@ -8,7 +8,7 @@ md5sum: f9cf5e375f7de81a406144a2c70cc64d - name: cat fastq fastqc_paired_end - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config tags: - cat - cat/fastq @@ -19,7 +19,7 @@ md5sum: f9cf5e375f7de81a406144a2c70cc64d - name: cat fastq single-end-same-name - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config tags: - cat - cat/fastq @@ -28,7 +28,7 @@ md5sum: 63f817db7a29a03eb538104495556f66 - name: cat fastq fastqc_paired_end_same_name - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config tags: - cat - cat/fastq @@ -39,7 +39,7 @@ md5sum: fe9f266f43a6fc3dcab690a18419a56e - name: cat fastq single-end-single-file - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_single_file -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end_single_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config tags: - cat - cat/fastq @@ -48,7 +48,7 @@ md5sum: e325ef7deb4023447a1f074e285761af - name: cat fastq single-end stub - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run tags: - cat - cat/fastq @@ -56,7 +56,7 @@ - path: ./output/cat/test.merged.fastq.gz - name: cat fastq fastqc_paired_end stub - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run tags: - cat - cat/fastq @@ -65,7 +65,7 @@ - path: ./output/cat/test_1.merged.fastq.gz - name: cat fastq single-end-same-name stub - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run tags: - cat - cat/fastq @@ -73,7 +73,7 @@ - path: ./output/cat/test.merged.fastq.gz - name: cat fastq fastqc_paired_end_same_name stub - command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cat/fastq/nextflow.config -stub-run tags: - cat - cat/fastq diff --git a/tests/modules/nf-core/cellranger/count/test.yml b/tests/modules/nf-core/cellranger/count/test.yml index 93e52c4a5fe..1621c1af39b 100644 --- a/tests/modules/nf-core/cellranger/count/test.yml +++ b/tests/modules/nf-core/cellranger/count/test.yml @@ -1,5 +1,5 @@ - name: cellranger count test_cellranger_count - command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/count/nextflow.config + command: nextflow run ./tests/modules/nf-core/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/count/nextflow.config tags: - cellranger/count - cellranger diff --git a/tests/modules/nf-core/cellranger/mkfastq/test.yml b/tests/modules/nf-core/cellranger/mkfastq/test.yml index 273d8fca029..dec205d6938 100644 --- a/tests/modules/nf-core/cellranger/mkfastq/test.yml +++ b/tests/modules/nf-core/cellranger/mkfastq/test.yml @@ -1,12 +1,12 @@ - name: cellranger mkfastq test_cellranger_mkfastq_simple - command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run tags: - cellranger - cellranger/mkfastq files: - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz - name: cellranger mkfastq test_cellranger_mkfastq_illumina - command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run tags: - cellranger - cellranger/mkfastq diff --git a/tests/modules/nf-core/cellranger/mkgtf/test.yml b/tests/modules/nf-core/cellranger/mkgtf/test.yml index 59eb9072654..b9ae76a7f9c 100644 --- a/tests/modules/nf-core/cellranger/mkgtf/test.yml +++ b/tests/modules/nf-core/cellranger/mkgtf/test.yml @@ -1,5 +1,5 @@ - name: cellranger mkgtf test_cellranger_mkgtf - command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkgtf/nextflow.config + command: nextflow run ./tests/modules/nf-core/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkgtf/nextflow.config tags: - cellranger/mkgtf - cellranger diff --git a/tests/modules/nf-core/cellranger/mkref/test.yml b/tests/modules/nf-core/cellranger/mkref/test.yml index 83ec5f9502e..6dea68de629 100644 --- a/tests/modules/nf-core/cellranger/mkref/test.yml +++ b/tests/modules/nf-core/cellranger/mkref/test.yml @@ -1,5 +1,5 @@ - name: cellranger mkref test_cellranger_mkref - command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config + command: nextflow run ./tests/modules/nf-core/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkref/nextflow.config tags: - cellranger/mkref - cellranger diff --git a/tests/modules/nf-core/centrifuge/centrifuge/test.yml b/tests/modules/nf-core/centrifuge/centrifuge/test.yml index 641ca7ef5e0..322e087865a 100644 --- a/tests/modules/nf-core/centrifuge/centrifuge/test.yml +++ b/tests/modules/nf-core/centrifuge/centrifuge/test.yml @@ -1,5 +1,5 @@ - name: centrifuge centrifuge test_centrifuge_centrifuge_single_end - command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c tests/config/nextflow.config tags: - centrifuge - centrifuge/centrifuge @@ -10,7 +10,7 @@ - path: output/centrifuge/versions.yml - name: centrifuge centrifuge test_centrifuge_centrifuge_paired_end - command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c tests/config/nextflow.config tags: - centrifuge - centrifuge/centrifuge diff --git a/tests/modules/nf-core/centrifuge/kreport/test.yml b/tests/modules/nf-core/centrifuge/kreport/test.yml index ab614c53982..d28da916edb 100644 --- a/tests/modules/nf-core/centrifuge/kreport/test.yml +++ b/tests/modules/nf-core/centrifuge/kreport/test.yml @@ -1,5 +1,5 @@ - name: centrifuge kreport test_centrifuge_kreport_single_end - command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c ./tests/config/nextflow.config -c ./tests/modules/centrifuge/kreport/nextflow.config + command: nextflow run ./tests/modules/nf-core/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/centrifuge/kreport/nextflow.config tags: - centrifuge/kreport - centrifuge @@ -9,7 +9,7 @@ - path: output/centrifuge/test.txt - name: centrifuge kreport test_centrifuge_kreport_paired_end - command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/centrifuge/kreport/nextflow.config + command: nextflow run ./tests/modules/nf-core/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/centrifuge/kreport/nextflow.config tags: - centrifuge/kreport - centrifuge diff --git a/tests/modules/nf-core/checkm/lineagewf/test.yml b/tests/modules/nf-core/checkm/lineagewf/test.yml index f81e8c9c0ee..8fcaf067293 100644 --- a/tests/modules/nf-core/checkm/lineagewf/test.yml +++ b/tests/modules/nf-core/checkm/lineagewf/test.yml @@ -1,5 +1,5 @@ - name: checkm lineagewf - command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c ./tests/config/nextflow.config -c ./tests/modules/checkm/lineagewf/nextflow.config + command: nextflow run ./tests/modules/nf-core/checkm/lineagewf -entry test_checkm_lineagewf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/checkm/lineagewf/nextflow.config tags: - checkm - checkm/lineagewf @@ -16,7 +16,7 @@ - "UID1" - name: checkm lineagewf_multi - command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c ./tests/config/nextflow.config -c ./tests/modules/checkm/lineagewf/nextflow.config + command: nextflow run ./tests/modules/nf-core/checkm/lineagewf -entry test_checkm_lineagewf_multi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/checkm/lineagewf/nextflow.config tags: - checkm - checkm/lineagewf diff --git a/tests/modules/nf-core/checkm/qa/test.yml b/tests/modules/nf-core/checkm/qa/test.yml index 0c3fa4c803b..bee7dedeb23 100644 --- a/tests/modules/nf-core/checkm/qa/test.yml +++ b/tests/modules/nf-core/checkm/qa/test.yml @@ -1,5 +1,5 @@ - name: checkm qa test_checkm_qa - command: nextflow run ./tests/modules/checkm/qa -entry test_checkm_qa -c ./tests/config/nextflow.config -c ./tests/modules/checkm/qa/nextflow.config + command: nextflow run ./tests/modules/nf-core/checkm/qa -entry test_checkm_qa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/checkm/qa/nextflow.config tags: - checkm/qa - checkm @@ -8,7 +8,7 @@ md5sum: 645f4282569afb4b171396732b2d2582 - name: checkm qa test_checkm_qa_fasta - command: nextflow run ./tests/modules/checkm/qa -entry test_checkm_qa_fasta -c ./tests/config/nextflow.config -c ./tests/modules/checkm/qa/nextflow.config + command: nextflow run ./tests/modules/nf-core/checkm/qa -entry test_checkm_qa_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/checkm/qa/nextflow.config tags: - checkm/qa - checkm diff --git a/tests/modules/nf-core/chromap/chromap/test.yml b/tests/modules/nf-core/chromap/chromap/test.yml index d089922ab79..073bcdcfe08 100644 --- a/tests/modules/nf-core/chromap/chromap/test.yml +++ b/tests/modules/nf-core/chromap/chromap/test.yml @@ -1,5 +1,5 @@ - name: chromap chromap test_chromap_chromap_single_end - command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_single_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config + command: nextflow run ./tests/modules/nf-core/chromap/chromap -entry test_chromap_chromap_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/chromap/nextflow.config tags: - chromap/chromap - chromap @@ -10,7 +10,7 @@ - path: output/chromap/versions.yml - name: chromap chromap test_chromap_chromap_paired_end - command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config + command: nextflow run ./tests/modules/nf-core/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/chromap/nextflow.config tags: - chromap/chromap - chromap @@ -21,7 +21,7 @@ - path: output/chromap/versions.yml - name: chromap chromap test_chromap_chromap_paired_bam - command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config + command: nextflow run ./tests/modules/nf-core/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/chromap/nextflow.config tags: - chromap/chromap - chromap diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml index 3e1d6fa60fe..d71767471d8 100644 --- a/tests/modules/nf-core/chromap/index/test.yml +++ b/tests/modules/nf-core/chromap/index/test.yml @@ -1,5 +1,5 @@ - name: chromap index test_chromap_index - command: nextflow run ./tests/modules/chromap/index -entry test_chromap_index -c ./tests/config/nextflow.config -c ./tests/modules/chromap/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/chromap/index -entry test_chromap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/chromap/index/nextflow.config tags: - chromap/index - chromap diff --git a/tests/modules/nf-core/clonalframeml/test.yml b/tests/modules/nf-core/clonalframeml/test.yml index 8ea11d164b9..1b880ec1a64 100644 --- a/tests/modules/nf-core/clonalframeml/test.yml +++ b/tests/modules/nf-core/clonalframeml/test.yml @@ -1,5 +1,5 @@ - name: clonalframeml test_clonalframeml - command: nextflow run ./tests/modules/clonalframeml -entry test_clonalframeml -c ./tests/config/nextflow.config -c ./tests/modules/clonalframeml/nextflow.config + command: nextflow run ./tests/modules/nf-core/clonalframeml -entry test_clonalframeml -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/clonalframeml/nextflow.config tags: - clonalframeml files: diff --git a/tests/modules/nf-core/cmseq/polymut/test.yml b/tests/modules/nf-core/cmseq/polymut/test.yml index 05887fa81a4..41ba04471bb 100644 --- a/tests/modules/nf-core/cmseq/polymut/test.yml +++ b/tests/modules/nf-core/cmseq/polymut/test.yml @@ -1,5 +1,5 @@ - name: cmseq polymut test_cmseq_polymut_1 - command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_1 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config + command: nextflow run ./tests/modules/nf-core/cmseq/polymut -entry test_cmseq_polymut_1 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cmseq/polymut/nextflow.config tags: - cmseq/polymut - cmseq @@ -8,7 +8,7 @@ md5sum: fd325c1724ee23d132a9115c64494efc - name: cmseq polymut test_cmseq_polymut_2 - command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_2 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config + command: nextflow run ./tests/modules/nf-core/cmseq/polymut -entry test_cmseq_polymut_2 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cmseq/polymut/nextflow.config tags: - cmseq/polymut - cmseq @@ -17,7 +17,7 @@ md5sum: fd325c1724ee23d132a9115c64494efc - name: cmseq polymut test_cmseq_polymut_3 - command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_3 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config + command: nextflow run ./tests/modules/nf-core/cmseq/polymut -entry test_cmseq_polymut_3 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cmseq/polymut/nextflow.config tags: - cmseq/polymut - cmseq diff --git a/tests/modules/nf-core/cnvkit/antitarget/test.yml b/tests/modules/nf-core/cnvkit/antitarget/test.yml index e1c3d0c8fce..2d0a4ce576f 100644 --- a/tests/modules/nf-core/cnvkit/antitarget/test.yml +++ b/tests/modules/nf-core/cnvkit/antitarget/test.yml @@ -1,5 +1,5 @@ - name: cnvkit antitarget test_cnvkit_antitarget - command: nextflow run ./tests/modules/cnvkit/antitarget -entry test_cnvkit_antitarget -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/antitarget/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/antitarget -entry test_cnvkit_antitarget -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/antitarget/nextflow.config tags: - cnvkit - cnvkit/antitarget diff --git a/tests/modules/nf-core/cnvkit/batch/test.yml b/tests/modules/nf-core/cnvkit/batch/test.yml index 006e142f292..4b14f412fd4 100755 --- a/tests/modules/nf-core/cnvkit/batch/test.yml +++ b/tests/modules/nf-core/cnvkit/batch/test.yml @@ -1,5 +1,5 @@ - name: cnvkit batch test_cnvkit_hybrid_somatic - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch @@ -27,7 +27,7 @@ md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7 - name: cnvkit batch test_cnvkit_wgs_somatic - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch @@ -57,7 +57,7 @@ md5sum: 6ae6b3fce7299eedca6133d911c38fe1 - name: cnvkit batch test_cnvkit_cram_wgs_somatic - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch @@ -87,7 +87,7 @@ md5sum: 6ae6b3fce7299eedca6133d911c38fe1 - name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch @@ -110,7 +110,7 @@ md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3 - name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch @@ -133,7 +133,7 @@ md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3 - name: cnvkit batch test_cnvkit_germline_hybrid_cram - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch @@ -158,7 +158,7 @@ md5sum: b4a49faf170e436ec32dcc21ccc3ce8f - name: cnvkit batch test_cnvkit_germline_hybrid_bam - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/batch/nextflow.config tags: - cnvkit - cnvkit/batch diff --git a/tests/modules/nf-core/cnvkit/reference/test.yml b/tests/modules/nf-core/cnvkit/reference/test.yml index a5baf0a2f7c..14b6d077b5f 100644 --- a/tests/modules/nf-core/cnvkit/reference/test.yml +++ b/tests/modules/nf-core/cnvkit/reference/test.yml @@ -1,5 +1,5 @@ - name: cnvkit reference test_cnvkit_reference - command: nextflow run ./tests/modules/cnvkit/reference -entry test_cnvkit_reference -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/reference/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvkit/reference -entry test_cnvkit_reference -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/reference/nextflow.config tags: - cnvkit/reference - cnvkit diff --git a/tests/modules/nf-core/cnvpytor/callcnvs/test.yml b/tests/modules/nf-core/cnvpytor/callcnvs/test.yml index fd07db4c21e..3ee825a01db 100644 --- a/tests/modules/nf-core/cnvpytor/callcnvs/test.yml +++ b/tests/modules/nf-core/cnvpytor/callcnvs/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor callcnvs test_cnvpytor_callcnvs - command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/callcnvs @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor callcnvs test_cnvpytor_callcnvs stub - command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/callcnvs diff --git a/tests/modules/nf-core/cnvpytor/histogram/test.yml b/tests/modules/nf-core/cnvpytor/histogram/test.yml index f67901d4158..aa10ac14f4a 100644 --- a/tests/modules/nf-core/cnvpytor/histogram/test.yml +++ b/tests/modules/nf-core/cnvpytor/histogram/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor histogram test_cnvpytor_histogram - command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/histogram @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor histogram test_cnvpytor_histogram stub - command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/histogram diff --git a/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml b/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml index a2530c26c12..ea1fed954c2 100644 --- a/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml +++ b/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth - command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/importreaddepth @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub - command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/importreaddepth @@ -17,7 +17,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram - command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/importreaddepth @@ -26,7 +26,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub - command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/importreaddepth diff --git a/tests/modules/nf-core/cnvpytor/partition/test.yml b/tests/modules/nf-core/cnvpytor/partition/test.yml index e24a1200b87..28a9651f96e 100644 --- a/tests/modules/nf-core/cnvpytor/partition/test.yml +++ b/tests/modules/nf-core/cnvpytor/partition/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor partition test_cnvpytor_partition - command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/partition @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor partition test_cnvpytor_partition stub - command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/partition diff --git a/tests/modules/nf-core/cnvpytor/view/test.yml b/tests/modules/nf-core/cnvpytor/view/test.yml index ea8ab792199..42307d52d38 100644 --- a/tests/modules/nf-core/cnvpytor/view/test.yml +++ b/tests/modules/nf-core/cnvpytor/view/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor view test_cnvpytor_view - command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/view @@ -9,7 +9,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor view test_cnvpytor_view tsv - command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_tsvout -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_tsvout -c tests/config/nextflow.config tags: - cnvpytor - cnvpytor/view @@ -18,7 +18,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor view test_cnvpytor_view stub - command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_stub -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_stub -c tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/view diff --git a/tests/modules/nf-core/controlfreec/assesssignificance/test.yml b/tests/modules/nf-core/controlfreec/assesssignificance/test.yml index 19e54acfe2a..4928e028d80 100644 --- a/tests/modules/nf-core/controlfreec/assesssignificance/test.yml +++ b/tests/modules/nf-core/controlfreec/assesssignificance/test.yml @@ -1,5 +1,5 @@ - name: controlfreec assesssignificance test_controlfreec_assesssignificance - command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c tests/config/nextflow.config tags: - controlfreec/assesssignificance - controlfreec @@ -9,7 +9,7 @@ - path: output/controlfreec/versions.yml - name: controlfreec assesssignificance test_controlfreec_assesssignificance_single - command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run tags: - controlfreec/assesssignificance - controlfreec diff --git a/tests/modules/nf-core/controlfreec/freec/test.yml b/tests/modules/nf-core/controlfreec/freec/test.yml index 1bd4e3a4265..df9fda5a4c8 100644 --- a/tests/modules/nf-core/controlfreec/freec/test.yml +++ b/tests/modules/nf-core/controlfreec/freec/test.yml @@ -1,5 +1,5 @@ - name: controlfreec test_controlfreec_freec - command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec -c tests/config/nextflow.config tags: - controlfreec - controlfreec/freec @@ -22,7 +22,7 @@ - path: output/controlfreec/versions.yml - name: controlfreec test_controlfreec_freec_single - command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run tags: - controlfreec - controlfreec/freec diff --git a/tests/modules/nf-core/controlfreec/freec2bed/test.yml b/tests/modules/nf-core/controlfreec/freec2bed/test.yml index 9abb3a545d7..4a97fbfc68e 100644 --- a/tests/modules/nf-core/controlfreec/freec2bed/test.yml +++ b/tests/modules/nf-core/controlfreec/freec2bed/test.yml @@ -1,5 +1,5 @@ - name: controlfreec freec2bed test_controlfreec_freec2bed - command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c tests/config/nextflow.config tags: - controlfreec/freec2bed - controlfreec @@ -8,7 +8,7 @@ md5sum: abe10b7ce94ba903503e697394c17297 - name: controlfreec freec2bed test_controlfreec_freec2bed_single - command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run tags: - controlfreec/freec2bed - controlfreec diff --git a/tests/modules/nf-core/controlfreec/freec2circos/test.yml b/tests/modules/nf-core/controlfreec/freec2circos/test.yml index c29111deb8f..2d0a807dd5b 100644 --- a/tests/modules/nf-core/controlfreec/freec2circos/test.yml +++ b/tests/modules/nf-core/controlfreec/freec2circos/test.yml @@ -1,5 +1,5 @@ - name: controlfreec freec2circos test_controlfreec_freec2circos - command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c tests/config/nextflow.config tags: - controlfreec - controlfreec/freec2circos @@ -8,7 +8,7 @@ md5sum: 19cf35f2c36b46f717dc8342b8a5a645 - name: controlfreec freec2circos test_controlfreec_freec2circos_single - command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run tags: - controlfreec - controlfreec/freec2circos diff --git a/tests/modules/nf-core/controlfreec/makegraph/test.yml b/tests/modules/nf-core/controlfreec/makegraph/test.yml index 02d1a165242..b51a1ca9c1b 100644 --- a/tests/modules/nf-core/controlfreec/makegraph/test.yml +++ b/tests/modules/nf-core/controlfreec/makegraph/test.yml @@ -1,5 +1,5 @@ - name: controlfreec makegraph test_controlfreec_makegraph - command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph -c tests/config/nextflow.config tags: - controlfreec - controlfreec/makegraph @@ -12,7 +12,7 @@ md5sum: 1435b29536b3b1555b4c423f8f4fb000 - name: controlfreec makegraph test_controlfreec_makegraph_single - command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run tags: - controlfreec - controlfreec/makegraph diff --git a/tests/modules/nf-core/cooler/cload/test.yml b/tests/modules/nf-core/cooler/cload/test.yml index f99f462411c..83552db836c 100644 --- a/tests/modules/nf-core/cooler/cload/test.yml +++ b/tests/modules/nf-core/cooler/cload/test.yml @@ -1,5 +1,5 @@ - name: cooler cload test_cooler_cload_pairix - command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_pairix -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/cload -entry test_cooler_cload_pairix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/cload/nextflow.config tags: - cooler/cload - cooler @@ -9,7 +9,7 @@ md5sum: 0cd85311089669688ec17468eae02111 - name: cooler cload test_cooler_cload_pairs - command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_pairs -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/cload -entry test_cooler_cload_pairs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/cload/nextflow.config tags: - cooler/cload - cooler @@ -19,7 +19,7 @@ md5sum: 7f832733fc7853ebb1937b33e4c1e0de - name: cooler cload test_cooler_cload_tabix - command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_tabix -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/cload -entry test_cooler_cload_tabix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/cload/nextflow.config tags: - cooler/cload - cooler diff --git a/tests/modules/nf-core/cooler/digest/test.yml b/tests/modules/nf-core/cooler/digest/test.yml index 80430ed7df9..3ddf058736b 100644 --- a/tests/modules/nf-core/cooler/digest/test.yml +++ b/tests/modules/nf-core/cooler/digest/test.yml @@ -1,5 +1,5 @@ - name: cooler digest test_cooler_digest - command: nextflow run ./tests/modules/cooler/digest -entry test_cooler_digest -c ./tests/config/nextflow.config -c ./tests/modules/cooler/digest/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/digest -entry test_cooler_digest -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/digest/nextflow.config tags: - cooler/digest - cooler diff --git a/tests/modules/nf-core/cooler/dump/test.yml b/tests/modules/nf-core/cooler/dump/test.yml index 6f81c7a9ea0..fa41e2eb018 100644 --- a/tests/modules/nf-core/cooler/dump/test.yml +++ b/tests/modules/nf-core/cooler/dump/test.yml @@ -1,5 +1,5 @@ - name: cooler dump test_cooler_dump - command: nextflow run ./tests/modules/cooler/dump -entry test_cooler_dump -c ./tests/config/nextflow.config -c ./tests/modules/cooler/dump/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/dump -entry test_cooler_dump -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/dump/nextflow.config tags: - cooler/dump - cooler diff --git a/tests/modules/nf-core/cooler/merge/test.yml b/tests/modules/nf-core/cooler/merge/test.yml index c884ba5eee5..735f94ab66f 100644 --- a/tests/modules/nf-core/cooler/merge/test.yml +++ b/tests/modules/nf-core/cooler/merge/test.yml @@ -1,5 +1,5 @@ - name: cooler merge test_cooler_merge - command: nextflow run ./tests/modules/cooler/merge -entry test_cooler_merge -c ./tests/config/nextflow.config -c ./tests/modules/cooler/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/merge -entry test_cooler_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/merge/nextflow.config tags: - cooler/merge - cooler diff --git a/tests/modules/nf-core/cooler/zoomify/test.yml b/tests/modules/nf-core/cooler/zoomify/test.yml index 3afdb8a6d7d..c39deee2baf 100644 --- a/tests/modules/nf-core/cooler/zoomify/test.yml +++ b/tests/modules/nf-core/cooler/zoomify/test.yml @@ -1,5 +1,5 @@ - name: cooler zoomify test_cooler_zoomify - command: nextflow run ./tests/modules/cooler/zoomify -entry test_cooler_zoomify -c ./tests/config/nextflow.config -c ./tests/modules/cooler/zoomify/nextflow.config + command: nextflow run ./tests/modules/nf-core/cooler/zoomify -entry test_cooler_zoomify -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cooler/zoomify/nextflow.config tags: - cooler - cooler/zoomify diff --git a/tests/modules/nf-core/csvtk/concat/test.yml b/tests/modules/nf-core/csvtk/concat/test.yml index 11a2af67d5a..08639640589 100644 --- a/tests/modules/nf-core/csvtk/concat/test.yml +++ b/tests/modules/nf-core/csvtk/concat/test.yml @@ -1,5 +1,5 @@ - name: csvtk concat - command: nextflow run ./tests/modules/csvtk/concat -entry test_csvtk_concat -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/concat/nextflow.config + command: nextflow run ./tests/modules/nf-core/csvtk/concat -entry test_csvtk_concat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/csvtk/concat/nextflow.config tags: - csvtk - csvtk/concat diff --git a/tests/modules/nf-core/csvtk/split/test.yml b/tests/modules/nf-core/csvtk/split/test.yml index bd13cca69d3..d9b1e85d671 100644 --- a/tests/modules/nf-core/csvtk/split/test.yml +++ b/tests/modules/nf-core/csvtk/split/test.yml @@ -1,5 +1,5 @@ - name: csvtk split test_csvtk_split_tsv - command: nextflow run ./tests/modules/csvtk/split -entry test_csvtk_split_tsv -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/split/nextflow.config + command: nextflow run ./tests/modules/nf-core/csvtk/split -entry test_csvtk_split_tsv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/csvtk/split/nextflow.config tags: - csvtk/split - csvtk @@ -12,7 +12,7 @@ md5sum: 45ae6da8111096746d1736d34220a3ec - name: csvtk split test_csvtk_split_csv - command: nextflow run ./tests/modules/csvtk/split -entry test_csvtk_split_csv -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/split/nextflow.config + command: nextflow run ./tests/modules/nf-core/csvtk/split -entry test_csvtk_split_csv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/csvtk/split/nextflow.config tags: - csvtk/split - csvtk diff --git a/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml b/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml index 363a12182f4..7a2fad5a374 100644 --- a/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml +++ b/tests/modules/nf-core/custom/dumpsoftwareversions/test.yml @@ -1,5 +1,5 @@ - name: custom dumpsoftwareversions - command: nextflow run ./tests/modules/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c ./tests/config/nextflow.config -c ./tests/modules/custom/dumpsoftwareversions/nextflow.config + command: nextflow run ./tests/modules/nf-core/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/dumpsoftwareversions/nextflow.config tags: - custom - custom/dumpsoftwareversions diff --git a/tests/modules/nf-core/custom/getchromsizes/test.yml b/tests/modules/nf-core/custom/getchromsizes/test.yml index f9cc652626f..bc870ff9dbf 100644 --- a/tests/modules/nf-core/custom/getchromsizes/test.yml +++ b/tests/modules/nf-core/custom/getchromsizes/test.yml @@ -1,5 +1,5 @@ - name: custom getchromsizes - command: nextflow run ./tests/modules/custom/getchromsizes -entry test_custom_getchromsizes -c ./tests/config/nextflow.config -c ./tests/modules/custom/getchromsizes/nextflow.config + command: nextflow run ./tests/modules/nf-core/custom/getchromsizes -entry test_custom_getchromsizes -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/getchromsizes/nextflow.config tags: - custom - custom/getchromsizes @@ -11,7 +11,7 @@ - path: output/custom/versions.yml md5sum: 3e4a23a0852f4ec34296224d87446d9a - name: custom getchromsizes_bgzip - command: nextflow run ./tests/modules/custom/getchromsizes -entry test_custom_getchromsizes_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/custom/getchromsizes/nextflow.config + command: nextflow run ./tests/modules/nf-core/custom/getchromsizes -entry test_custom_getchromsizes_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/getchromsizes/nextflow.config tags: - custom - custom/getchromsizes diff --git a/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml b/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml index df3cd9363d7..beb1580fe0e 100644 --- a/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml +++ b/tests/modules/nf-core/custom/sratoolsncbisettings/test.yml @@ -1,5 +1,5 @@ - name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_good_existing" - command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config + command: nextflow run ./tests/modules/nf-core/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config tags: - "custom" - "custom/sratoolsncbisettings" @@ -11,7 +11,7 @@ - "sratools: 2.11.0" - name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_bad_existing" - command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config + command: nextflow run ./tests/modules/nf-core/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config tags: - "custom" - "custom/sratoolsncbisettings" @@ -30,7 +30,7 @@ should_exist: false - name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_nonexisting" - command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow.config + command: nextflow run ./tests/modules/nf-core/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/custom/sratoolsncbisettings/nextflow.config tags: - "custom" - "custom/sratoolsncbisettings" diff --git a/tests/modules/nf-core/cutadapt/test.yml b/tests/modules/nf-core/cutadapt/test.yml index 6fa0eb4fb2d..94c0715b706 100644 --- a/tests/modules/nf-core/cutadapt/test.yml +++ b/tests/modules/nf-core/cutadapt/test.yml @@ -1,5 +1,5 @@ - name: cutadapt single-end - command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cutadapt/nextflow.config + command: nextflow run ./tests/modules/nf-core/cutadapt -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cutadapt/nextflow.config tags: - cutadapt files: @@ -7,7 +7,7 @@ - path: ./output/cutadapt/test.trim.fastq.gz - name: cutadapt paired-end - command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cutadapt/nextflow.config + command: nextflow run ./tests/modules/nf-core/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cutadapt/nextflow.config tags: - cutadapt files: diff --git a/tests/modules/nf-core/damageprofiler/test.yml b/tests/modules/nf-core/damageprofiler/test.yml index 5760ee2c457..bbaa31c0f82 100644 --- a/tests/modules/nf-core/damageprofiler/test.yml +++ b/tests/modules/nf-core/damageprofiler/test.yml @@ -1,5 +1,5 @@ - name: damageprofiler test_damageprofiler - command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config + command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/damageprofiler/nextflow.config tags: - damageprofiler files: @@ -34,7 +34,7 @@ md5sum: 25119c0fcc8839fdbb3ed10922fb07f4 - name: damageprofiler test_damageprofiler_reference - command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config + command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/damageprofiler/nextflow.config tags: - damageprofiler files: @@ -69,7 +69,7 @@ md5sum: 25119c0fcc8839fdbb3ed10922fb07f4 - name: damageprofiler test_damageprofiler_specieslist - command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config + command: nextflow run ./tests/modules/nf-core/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/damageprofiler/nextflow.config tags: - damageprofiler files: diff --git a/tests/modules/nf-core/dastool/dastool/test.yml b/tests/modules/nf-core/dastool/dastool/test.yml index cda17bda686..d802cbba8e1 100644 --- a/tests/modules/nf-core/dastool/dastool/test.yml +++ b/tests/modules/nf-core/dastool/dastool/test.yml @@ -1,5 +1,5 @@ - name: dastool dastool test_dastool_dastool - command: nextflow run tests/modules/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config tags: - dastool/dastool - dastool diff --git a/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml b/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml index 948814389ff..6c6dd8a652f 100644 --- a/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml +++ b/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml @@ -1,5 +1,5 @@ - name: dastool fastatocontig2bin test_dastool_fastatocontig2bin - command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config tags: - dastool - dastool/fastatocontig2bin @@ -10,7 +10,7 @@ md5sum: ff4b6f14bee4548bf09b5e602c306595 - name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped - command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config tags: - dastool - dastool/fastatocontig2bin diff --git a/tests/modules/nf-core/dastool/scaffolds2bin/test.yml b/tests/modules/nf-core/dastool/scaffolds2bin/test.yml index 3d91c8c10af..40e73615e47 100644 --- a/tests/modules/nf-core/dastool/scaffolds2bin/test.yml +++ b/tests/modules/nf-core/dastool/scaffolds2bin/test.yml @@ -1,5 +1,5 @@ - name: dastool scaffolds2bin test_dastool_scaffolds2bin - command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config tags: - dastool - dastool/scaffolds2bin @@ -9,7 +9,7 @@ - path: output/dastool/versions.yml md5sum: d0831ed159eb5a1a1565d1d211012ad6 - name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped - command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config tags: - dastool - dastool/scaffolds2bin diff --git a/tests/modules/nf-core/dedup/test.yml b/tests/modules/nf-core/dedup/test.yml index 077aac0dc4d..0d9445f8fdb 100644 --- a/tests/modules/nf-core/dedup/test.yml +++ b/tests/modules/nf-core/dedup/test.yml @@ -1,5 +1,5 @@ - name: dedup test_dedup - command: nextflow run ./tests/modules/dedup -entry test_dedup -c ./tests/config/nextflow.config -c ./tests/modules/dedup/nextflow.config + command: nextflow run ./tests/modules/nf-core/dedup -entry test_dedup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dedup/nextflow.config tags: - dedup files: diff --git a/tests/modules/nf-core/deeparg/downloaddata/test.yml b/tests/modules/nf-core/deeparg/downloaddata/test.yml index c5c99de22e8..1a4b08f6351 100644 --- a/tests/modules/nf-core/deeparg/downloaddata/test.yml +++ b/tests/modules/nf-core/deeparg/downloaddata/test.yml @@ -1,5 +1,5 @@ - name: deeparg downloaddata test_deeparg_downloaddata - command: nextflow run tests/modules/deeparg/downloaddata -entry test_deeparg_downloaddata -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeparg/downloaddata -entry test_deeparg_downloaddata -c tests/config/nextflow.config tags: - deeparg - deeparg/downloaddata diff --git a/tests/modules/nf-core/deeparg/predict/test.yml b/tests/modules/nf-core/deeparg/predict/test.yml index e3a15411069..20977ce28c4 100644 --- a/tests/modules/nf-core/deeparg/predict/test.yml +++ b/tests/modules/nf-core/deeparg/predict/test.yml @@ -1,5 +1,5 @@ - name: deeparg predict test_deeparg_predict - command: nextflow run tests/modules/deeparg/predict -entry test_deeparg_predict -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeparg/predict -entry test_deeparg_predict -c tests/config/nextflow.config tags: - deeparg/predict - deeparg diff --git a/tests/modules/nf-core/deepbgc/download/test.yml b/tests/modules/nf-core/deepbgc/download/test.yml index bae68f67ed5..aa71b99596f 100644 --- a/tests/modules/nf-core/deepbgc/download/test.yml +++ b/tests/modules/nf-core/deepbgc/download/test.yml @@ -1,5 +1,5 @@ - name: deepbgc download test_deepbgc_download - command: nextflow run ./tests/modules/deepbgc/download -entry test_deepbgc_download -c ./tests/config/nextflow.config -c ./tests/modules/deepbgc/download/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepbgc/download -entry test_deepbgc_download -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deepbgc/download/nextflow.config tags: - deepbgc - deepbgc/download diff --git a/tests/modules/nf-core/deepbgc/pipeline/test.yml b/tests/modules/nf-core/deepbgc/pipeline/test.yml index eea38831849..0923aad76b7 100644 --- a/tests/modules/nf-core/deepbgc/pipeline/test.yml +++ b/tests/modules/nf-core/deepbgc/pipeline/test.yml @@ -1,5 +1,5 @@ - name: deepbgc pipeline test_deepbgc_pipeline_gbk - command: nextflow run ./tests/modules/deepbgc/pipeline -entry test_deepbgc_pipeline_gbk -c ./tests/config/nextflow.config -c ./tests/modules/deepbgc/pipeline/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepbgc/pipeline -entry test_deepbgc_pipeline_gbk -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deepbgc/pipeline/nextflow.config tags: - deepbgc/pipeline - deepbgc @@ -47,7 +47,7 @@ md5sum: 8fe56fcf4d9e839e83be7523cd3efa02 - name: deepbgc pipeline test_deepbgc_pipeline_fa - command: nextflow run ./tests/modules/deepbgc/pipeline -entry test_deepbgc_pipeline_fa -c ./tests/config/nextflow.config -c ./tests/modules/deepbgc/pipeline/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepbgc/pipeline -entry test_deepbgc_pipeline_fa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deepbgc/pipeline/nextflow.config tags: - deepbgc/pipeline - deepbgc diff --git a/tests/modules/nf-core/deeptools/bamcoverage/test.yml b/tests/modules/nf-core/deeptools/bamcoverage/test.yml index 63ef6442007..e777e6a87cc 100644 --- a/tests/modules/nf-core/deeptools/bamcoverage/test.yml +++ b/tests/modules/nf-core/deeptools/bamcoverage/test.yml @@ -1,5 +1,5 @@ - name: deeptools bamcoverage test_deeptools_bamcoverage_bam - command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/bamcoverage/nextflow.config tags: - deeptools/bamcoverage - deeptools @@ -8,7 +8,7 @@ md5sum: 95fe9383a9e6c02aea6b785cf074274f - name: deeptools bamcoverage test_deeptools_bamcoverage_cram - command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/bamcoverage/nextflow.config tags: - deeptools/bamcoverage - deeptools @@ -17,7 +17,7 @@ md5sum: 95fe9383a9e6c02aea6b785cf074274f - name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai - command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/bamcoverage/nextflow.config tags: - deeptools/bamcoverage - deeptools diff --git a/tests/modules/nf-core/deeptools/computematrix/test.yml b/tests/modules/nf-core/deeptools/computematrix/test.yml index 88657de3ef0..b49144f6836 100644 --- a/tests/modules/nf-core/deeptools/computematrix/test.yml +++ b/tests/modules/nf-core/deeptools/computematrix/test.yml @@ -1,5 +1,5 @@ - name: deeptools computematrix - command: nextflow run ./tests/modules/deeptools/computematrix -entry test_deeptools_computematrix -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/computematrix/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/computematrix -entry test_deeptools_computematrix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/computematrix/nextflow.config tags: - deeptools - deeptools/computematrix diff --git a/tests/modules/nf-core/deeptools/plotfingerprint/test.yml b/tests/modules/nf-core/deeptools/plotfingerprint/test.yml index 11d4ae7b92f..080c595b02c 100644 --- a/tests/modules/nf-core/deeptools/plotfingerprint/test.yml +++ b/tests/modules/nf-core/deeptools/plotfingerprint/test.yml @@ -1,5 +1,5 @@ - name: deeptools plotfingerprint - command: nextflow run ./tests/modules/deeptools/plotfingerprint -entry test_deeptools_plotfingerprint -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotfingerprint/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/plotfingerprint -entry test_deeptools_plotfingerprint -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/plotfingerprint/nextflow.config tags: - deeptools - deeptools/plotfingerprint diff --git a/tests/modules/nf-core/deeptools/plotheatmap/test.yml b/tests/modules/nf-core/deeptools/plotheatmap/test.yml index ddc468e29d0..eaad3135faa 100644 --- a/tests/modules/nf-core/deeptools/plotheatmap/test.yml +++ b/tests/modules/nf-core/deeptools/plotheatmap/test.yml @@ -1,5 +1,5 @@ - name: deeptools plotheatmap - command: nextflow run ./tests/modules/deeptools/plotheatmap -entry test_deeptools_plotheatmap -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotheatmap/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/plotheatmap -entry test_deeptools_plotheatmap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/plotheatmap/nextflow.config tags: - deeptools - deeptools/plotheatmap diff --git a/tests/modules/nf-core/deeptools/plotprofile/test.yml b/tests/modules/nf-core/deeptools/plotprofile/test.yml index 4b6c5b9afc4..1c457ab93e3 100644 --- a/tests/modules/nf-core/deeptools/plotprofile/test.yml +++ b/tests/modules/nf-core/deeptools/plotprofile/test.yml @@ -1,5 +1,5 @@ - name: deeptools plotprofile - command: nextflow run ./tests/modules/deeptools/plotprofile -entry test_deeptools_plotprofile -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotprofile/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeptools/plotprofile -entry test_deeptools_plotprofile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/deeptools/plotprofile/nextflow.config tags: - deeptools - deeptools/plotprofile diff --git a/tests/modules/nf-core/deepvariant/test.yml b/tests/modules/nf-core/deepvariant/test.yml index 30a0b1b32a4..88f377fd566 100644 --- a/tests/modules/nf-core/deepvariant/test.yml +++ b/tests/modules/nf-core/deepvariant/test.yml @@ -1,5 +1,5 @@ - name: deepvariant test_deepvariant - command: nextflow run tests/modules/deepvariant -entry test_deepvariant -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant -c tests/config/nextflow.config tags: - deepvariant files: @@ -11,7 +11,7 @@ md5sum: 51572055ca5c07fc4001b25a9c273bf8 - name: deepvariant test_deepvariant_cram_intervals - command: nextflow run tests/modules/deepvariant -entry test_deepvariant_cram_intervals -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant_cram_intervals -c tests/config/nextflow.config tags: - deepvariant files: diff --git a/tests/modules/nf-core/delly/call/test.yml b/tests/modules/nf-core/delly/call/test.yml index c3490a76146..0b1564c12a6 100644 --- a/tests/modules/nf-core/delly/call/test.yml +++ b/tests/modules/nf-core/delly/call/test.yml @@ -1,5 +1,5 @@ - name: delly call test_delly_call_bam - command: nextflow run ./tests/modules/delly/call -entry test_delly_call_bam -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config + command: nextflow run ./tests/modules/nf-core/delly/call -entry test_delly_call_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/delly/call/nextflow.config tags: - delly - delly/call @@ -10,7 +10,7 @@ md5sum: c198abfc14584c5ac69c004057927e0b - name: delly call test_delly_call_cram - command: nextflow run ./tests/modules/delly/call -entry test_delly_call_cram -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config + command: nextflow run ./tests/modules/nf-core/delly/call -entry test_delly_call_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/delly/call/nextflow.config tags: - delly - delly/call @@ -21,7 +21,7 @@ md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271 - name: delly call test_delly_call_exclude_regions - command: nextflow run ./tests/modules/delly/call -entry test_delly_call_exclude_regions -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config + command: nextflow run ./tests/modules/nf-core/delly/call -entry test_delly_call_exclude_regions -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/delly/call/nextflow.config tags: - delly - delly/call diff --git a/tests/modules/nf-core/diamond/blastp/test.yml b/tests/modules/nf-core/diamond/blastp/test.yml index aff4e1c5637..73e983cf8cf 100644 --- a/tests/modules/nf-core/diamond/blastp/test.yml +++ b/tests/modules/nf-core/diamond/blastp/test.yml @@ -1,5 +1,5 @@ - name: diamond blastp test_diamond_blastp - command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config tags: - diamond/blastp - diamond @@ -8,7 +8,7 @@ - path: output/diamond/versions.yml - name: diamond blastp test_diamond_blastp_daa - command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config tags: - diamond/blastp - diamond diff --git a/tests/modules/nf-core/diamond/blastx/test.yml b/tests/modules/nf-core/diamond/blastx/test.yml index 9f62d2ef7e3..adbdff9a14c 100644 --- a/tests/modules/nf-core/diamond/blastx/test.yml +++ b/tests/modules/nf-core/diamond/blastx/test.yml @@ -1,5 +1,5 @@ - name: diamond blastx test_diamond_blastx - command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/diamond/blastx/nextflow.config tags: - diamond - diamond/blastx @@ -10,7 +10,7 @@ - path: output/diamond/test.diamond_blastx.txt - name: diamond blastx test_diamond_blastx_daa - command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/diamond/blastx/nextflow.config tags: - diamond - diamond/blastx diff --git a/tests/modules/nf-core/diamond/makedb/test.yml b/tests/modules/nf-core/diamond/makedb/test.yml index cdddf735296..5631872e133 100644 --- a/tests/modules/nf-core/diamond/makedb/test.yml +++ b/tests/modules/nf-core/diamond/makedb/test.yml @@ -1,5 +1,5 @@ - name: diamond makedb test_diamond_makedb - command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config tags: - diamond/makedb - diamond diff --git a/tests/modules/nf-core/dragmap/align/test.yml b/tests/modules/nf-core/dragmap/align/test.yml index b0196e554c8..bfc23508118 100644 --- a/tests/modules/nf-core/dragmap/align/test.yml +++ b/tests/modules/nf-core/dragmap/align/test.yml @@ -1,5 +1,5 @@ - name: dragmap align single-end - command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config tags: - dragmap - dragmap/align @@ -8,7 +8,7 @@ - path: output/dragmap/test.dragmap.log - name: dragmap align single-end_sort - command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config tags: - dragmap - dragmap/align @@ -17,7 +17,7 @@ - path: output/dragmap/test.dragmap.log - name: dragmap align paired-end - command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config tags: - dragmap - dragmap/align @@ -26,7 +26,7 @@ - path: output/dragmap/test.dragmap.log - name: dragmap align paired-end_sort - command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragmap/align -entry test_dragmap_align_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/align/nextflow.config tags: - dragmap - dragmap/align diff --git a/tests/modules/nf-core/dragmap/hashtable/test.yml b/tests/modules/nf-core/dragmap/hashtable/test.yml index 0534bdc2ca9..553799047b2 100644 --- a/tests/modules/nf-core/dragmap/hashtable/test.yml +++ b/tests/modules/nf-core/dragmap/hashtable/test.yml @@ -1,5 +1,5 @@ - name: dragmap hashtable - command: nextflow run ./tests/modules/dragmap/hashtable -entry test_dragmap_hashtable -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/hashtable/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragmap/hashtable -entry test_dragmap_hashtable -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragmap/hashtable/nextflow.config tags: - dragmap - dragmap/hashtable diff --git a/tests/modules/nf-core/dragonflye/test.yml b/tests/modules/nf-core/dragonflye/test.yml index ef9121ba6ec..47a3ce8d41f 100644 --- a/tests/modules/nf-core/dragonflye/test.yml +++ b/tests/modules/nf-core/dragonflye/test.yml @@ -1,5 +1,5 @@ - name: dragonflye with miniasm - command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye -c ./tests/config/nextflow.config -c ./tests/modules/dragonflye/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragonflye -entry test_dragonflye -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragonflye/nextflow.config tags: - dragonflye files: @@ -12,7 +12,7 @@ - path: output/dragonflye/dragonflye.log - name: dragonflye with raven - command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye_raven -c ./tests/config/nextflow.config -c ./tests/modules/dragonflye/nextflow.config + command: nextflow run ./tests/modules/nf-core/dragonflye -entry test_dragonflye_raven -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dragonflye/nextflow.config tags: - dragonflye files: diff --git a/tests/modules/nf-core/dshbio/exportsegments/test.yml b/tests/modules/nf-core/dshbio/exportsegments/test.yml index 85406f8f354..aaf46bd6eb7 100644 --- a/tests/modules/nf-core/dshbio/exportsegments/test.yml +++ b/tests/modules/nf-core/dshbio/exportsegments/test.yml @@ -1,5 +1,5 @@ - name: dshbio exportsegments - command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config tags: - dshbio - dshbio/exportsegments @@ -8,7 +8,7 @@ md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c - name: dshbio exportsegments bgz - command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_bgz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments_bgz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config tags: - dshbio - dshbio/exportsegments @@ -17,7 +17,7 @@ md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c - name: dshbio exportsegments gz - command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_gz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config tags: - dshbio - dshbio/exportsegments @@ -26,7 +26,7 @@ md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c - name: dshbio exportsegments zst - command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_zst -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/exportsegments -entry test_dshbio_exportsegments_zst -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/exportsegments/nextflow.config tags: - dshbio - dshbio/exportsegments diff --git a/tests/modules/nf-core/dshbio/filterbed/test.yml b/tests/modules/nf-core/dshbio/filterbed/test.yml index 278fd5a375a..5c87e42926d 100644 --- a/tests/modules/nf-core/dshbio/filterbed/test.yml +++ b/tests/modules/nf-core/dshbio/filterbed/test.yml @@ -1,5 +1,5 @@ - name: dshbio filterbed - command: nextflow run ./tests/modules/dshbio/filterbed -entry test_dshbio_filterbed -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/filterbed/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/filterbed -entry test_dshbio_filterbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/filterbed/nextflow.config tags: - dshbio - dshbio/filterbed diff --git a/tests/modules/nf-core/dshbio/filtergff3/test.yml b/tests/modules/nf-core/dshbio/filtergff3/test.yml index 43238333c6b..0a649dc1571 100644 --- a/tests/modules/nf-core/dshbio/filtergff3/test.yml +++ b/tests/modules/nf-core/dshbio/filtergff3/test.yml @@ -1,5 +1,5 @@ - name: dshbio filtergff3 - command: nextflow run ./tests/modules/dshbio/filtergff3 -entry test_dshbio_filtergff3 -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/filtergff3/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/filtergff3 -entry test_dshbio_filtergff3 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/filtergff3/nextflow.config tags: - dshbio - dshbio/filtergff3 diff --git a/tests/modules/nf-core/dshbio/splitbed/test.yml b/tests/modules/nf-core/dshbio/splitbed/test.yml index ab14648eb22..6d0a8ee654e 100644 --- a/tests/modules/nf-core/dshbio/splitbed/test.yml +++ b/tests/modules/nf-core/dshbio/splitbed/test.yml @@ -1,5 +1,5 @@ - name: dshbio splitbed - command: nextflow run ./tests/modules/dshbio/splitbed -entry test_dshbio_splitbed -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/splitbed/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/splitbed -entry test_dshbio_splitbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/splitbed/nextflow.config tags: - dshbio - dshbio/splitbed diff --git a/tests/modules/nf-core/dshbio/splitgff3/test.yml b/tests/modules/nf-core/dshbio/splitgff3/test.yml index 6087ce111ee..1302afd42ee 100644 --- a/tests/modules/nf-core/dshbio/splitgff3/test.yml +++ b/tests/modules/nf-core/dshbio/splitgff3/test.yml @@ -1,5 +1,5 @@ - name: dshbio splitgff3 - command: nextflow run ./tests/modules/dshbio/splitgff3 -entry test_dshbio_splitgff3 -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/splitgff3/nextflow.config + command: nextflow run ./tests/modules/nf-core/dshbio/splitgff3 -entry test_dshbio_splitgff3 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/dshbio/splitgff3/nextflow.config tags: - dshbio - dshbio/splitgff3 diff --git a/tests/modules/nf-core/ectyper/test.yml b/tests/modules/nf-core/ectyper/test.yml index 15e0327da0d..16970b3d3c5 100644 --- a/tests/modules/nf-core/ectyper/test.yml +++ b/tests/modules/nf-core/ectyper/test.yml @@ -1,5 +1,5 @@ - name: ectyper test_ectyper - command: nextflow run ./tests/modules/ectyper -entry test_ectyper -c ./tests/config/nextflow.config -c ./tests/modules/ectyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/ectyper -entry test_ectyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ectyper/nextflow.config tags: - ectyper files: diff --git a/tests/modules/nf-core/eido/convert/test.yml b/tests/modules/nf-core/eido/convert/test.yml index 8015c1149af..11cdb157b3e 100644 --- a/tests/modules/nf-core/eido/convert/test.yml +++ b/tests/modules/nf-core/eido/convert/test.yml @@ -1,5 +1,5 @@ - name: eido convert test_eido_convert_nextflow_samplesheet - command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config -c ./tests/modules/eido/convert/nextflow.config + command: nextflow run ./tests/modules/nf-core/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/eido/convert/nextflow.config tags: - eido/convert - eido @@ -8,7 +8,7 @@ md5sum: 7aa4da4944650b9c7c451c5dfbeae663 - name: eido convert test_eido_convert_pep_project - command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config -c ./tests/modules/eido/convert/nextflow.config + command: nextflow run ./tests/modules/nf-core/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/eido/convert/nextflow.config tags: - eido/convert - eido diff --git a/tests/modules/nf-core/eido/validate/test.yml b/tests/modules/nf-core/eido/validate/test.yml index 03a4e5b2a35..5071faa502c 100644 --- a/tests/modules/nf-core/eido/validate/test.yml +++ b/tests/modules/nf-core/eido/validate/test.yml @@ -1,5 +1,5 @@ - name: eido validate test_eido_validate_on_nextflow_samplesheet - command: nextflow run ./tests/modules/eido/validate -entry test_eido_validate_on_nextflow_samplesheet -c ./tests/config/nextflow.config -c ./tests/modules/eido/validate/nextflow.config + command: nextflow run ./tests/modules/nf-core/eido/validate -entry test_eido_validate_on_nextflow_samplesheet -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/eido/validate/nextflow.config tags: - eido/validate - eido @@ -8,7 +8,7 @@ md5sum: 3a197c21ebf411aac7616bf9b4470de3 - name: eido validate test_eido_validate_on_pep_config - command: nextflow run ./tests/modules/eido/validate -entry test_eido_validate_on_pep_config -c ./tests/config/nextflow.config -c ./tests/modules/eido/validate/nextflow.config + command: nextflow run ./tests/modules/nf-core/eido/validate -entry test_eido_validate_on_pep_config -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/eido/validate/nextflow.config tags: - eido/validate - eido diff --git a/tests/modules/nf-core/elprep/filter/test.yml b/tests/modules/nf-core/elprep/filter/test.yml index 922d7a9b777..835febf5c51 100644 --- a/tests/modules/nf-core/elprep/filter/test.yml +++ b/tests/modules/nf-core/elprep/filter/test.yml @@ -1,5 +1,5 @@ - name: elprep filter test_elprep_filter - command: nextflow run tests/modules/elprep/filter -entry test_elprep_filter -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/elprep/filter -entry test_elprep_filter -c tests/config/nextflow.config tags: - elprep - elprep/filter diff --git a/tests/modules/nf-core/elprep/merge/test.yml b/tests/modules/nf-core/elprep/merge/test.yml index ad2ecfefd4f..11560b284cb 100644 --- a/tests/modules/nf-core/elprep/merge/test.yml +++ b/tests/modules/nf-core/elprep/merge/test.yml @@ -1,5 +1,5 @@ - name: elprep merge test_elprep_merge - command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config tags: - elprep - elprep/merge diff --git a/tests/modules/nf-core/elprep/split/test.yml b/tests/modules/nf-core/elprep/split/test.yml index 2de3f99bd18..382e0dd4adc 100644 --- a/tests/modules/nf-core/elprep/split/test.yml +++ b/tests/modules/nf-core/elprep/split/test.yml @@ -1,5 +1,5 @@ - name: elprep split test_elprep_split - command: nextflow run tests/modules/elprep/split -entry test_elprep_split -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/elprep/split -entry test_elprep_split -c tests/config/nextflow.config tags: - elprep - elprep/split diff --git a/tests/modules/nf-core/emboss/seqret/test.yml b/tests/modules/nf-core/emboss/seqret/test.yml index b98ccdbd1b6..ac6c9ea0712 100644 --- a/tests/modules/nf-core/emboss/seqret/test.yml +++ b/tests/modules/nf-core/emboss/seqret/test.yml @@ -1,5 +1,5 @@ - name: emboss seqret test_emboss_seqret_gb2embl - command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2embl -c ./tests/config/nextflow.config -c ./tests/modules/emboss/seqret/nextflow.config + command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2embl -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/emboss/seqret/nextflow.config tags: - emboss - emboss/seqret @@ -9,7 +9,7 @@ contains: ["ID NZ_CP069563;"] # Human-readable test for correct format and sequence - name: emboss seqret test_emboss_seqret_gb2gff - command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2gff -c ./tests/config/nextflow.config -c ./tests/modules/emboss/seqret/nextflow.config + command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2gff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/emboss/seqret/nextflow.config tags: - emboss - emboss/seqret @@ -20,7 +20,7 @@ - ">NZ_CP069563" # Human-readable test for correct sequence - name: emboss seqret test_emboss_seqret_gb2pir - command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2pir -c ./tests/config/nextflow.config -c ./tests/modules/emboss/seqret/nextflow.config + command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2pir -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/emboss/seqret/nextflow.config tags: - emboss - emboss/seqret @@ -30,7 +30,7 @@ contains: [">D1;NZ_CP069563"] # Human-readable test for correct format and sequence - name: emboss seqret test_emboss_seqret_gb2fasta - command: nextflow run ./tests/modules/emboss/seqret -entry test_emboss_seqret_gb2fasta -c ./tests/config/nextflow.config -c ./tests/modules/emboss/seqret/nextflow.config + command: nextflow run ./tests/modules/nf-core/emboss/seqret -entry test_emboss_seqret_gb2fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/emboss/seqret/nextflow.config tags: - emboss - emboss/seqret diff --git a/tests/modules/nf-core/emmtyper/test.yml b/tests/modules/nf-core/emmtyper/test.yml index 81854eb6528..61b53fd3118 100644 --- a/tests/modules/nf-core/emmtyper/test.yml +++ b/tests/modules/nf-core/emmtyper/test.yml @@ -1,5 +1,5 @@ - name: emmtyper test_emmtyper - command: nextflow run ./tests/modules/emmtyper -entry test_emmtyper -c ./tests/config/nextflow.config -c ./tests/modules/emmtyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/emmtyper -entry test_emmtyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/emmtyper/nextflow.config tags: - emmtyper files: diff --git a/tests/modules/nf-core/endorspy/test.yml b/tests/modules/nf-core/endorspy/test.yml index 1369227f404..f81f8e88588 100644 --- a/tests/modules/nf-core/endorspy/test.yml +++ b/tests/modules/nf-core/endorspy/test.yml @@ -1,5 +1,5 @@ - name: endorspy test_endorspy - command: nextflow run ./tests/modules/endorspy -entry test_endorspy -c ./tests/config/nextflow.config -c ./tests/modules/endorspy/nextflow.config + command: nextflow run ./tests/modules/nf-core/endorspy -entry test_endorspy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/endorspy/nextflow.config tags: - endorspy files: diff --git a/tests/modules/nf-core/ensemblvep/test.yml b/tests/modules/nf-core/ensemblvep/test.yml index dedd56195b6..5c3f4fccf44 100644 --- a/tests/modules/nf-core/ensemblvep/test.yml +++ b/tests/modules/nf-core/ensemblvep/test.yml @@ -1,5 +1,5 @@ - name: ensemblvep test_ensemblvep_fasta_json - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -7,7 +7,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_fasta_tab - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -15,7 +15,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_fasta_vcf - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -23,7 +23,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_fasta_vcf_bgzip - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -31,7 +31,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_fasta_vcf_gzip - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf_gzip -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf_gzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -39,7 +39,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_fasta - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -47,7 +47,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_no_fasta - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config tags: - ensemblvep files: @@ -55,7 +55,7 @@ - path: output/ensemblvep/test.summary.html - name: ensemblvep test_ensemblvep_fasta_vcf_stub - command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config -stub + command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config -stub tags: - ensemblvep files: diff --git a/tests/modules/nf-core/entrezdirect/esearch/test.yml b/tests/modules/nf-core/entrezdirect/esearch/test.yml index 05372422f24..0dbe1e31df3 100644 --- a/tests/modules/nf-core/entrezdirect/esearch/test.yml +++ b/tests/modules/nf-core/entrezdirect/esearch/test.yml @@ -1,5 +1,5 @@ - name: entrezdirect esearch test_entrezdirect_esearch_pubmed - command: nextflow run ./tests/modules/entrezdirect/esearch -entry test_entrezdirect_esearch_pubmed -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esearch/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/esearch -entry test_entrezdirect_esearch_pubmed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/esearch/nextflow.config tags: - entrezdirect/esearch - entrezdirect @@ -15,7 +15,7 @@ - "" - name: entrezdirect esearch test_entrezdirect_esearch_genome - command: nextflow run ./tests/modules/entrezdirect/esearch -entry test_entrezdirect_esearch_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esearch/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/esearch -entry test_entrezdirect_esearch_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/esearch/nextflow.config tags: - entrezdirect/esearch - entrezdirect @@ -31,7 +31,7 @@ - "" - name: entrezdirect esearch test_entrezdirect_esearch_assembly - command: nextflow run ./tests/modules/entrezdirect/esearch -entry test_entrezdirect_esearch_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esearch/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/esearch -entry test_entrezdirect_esearch_assembly -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/esearch/nextflow.config tags: - entrezdirect/esearch - entrezdirect diff --git a/tests/modules/nf-core/entrezdirect/esummary/test.yml b/tests/modules/nf-core/entrezdirect/esummary/test.yml index 06618ec6d44..635a9449233 100644 --- a/tests/modules/nf-core/entrezdirect/esummary/test.yml +++ b/tests/modules/nf-core/entrezdirect/esummary/test.yml @@ -1,5 +1,5 @@ - name: entrezdirect esummary test_entrezdirect_esummary_sra - command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_sra -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/esummary -entry test_entrezdirect_esummary_sra -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/esummary/nextflow.config tags: - entrezdirect - entrezdirect/esummary @@ -8,7 +8,7 @@ contains: ["WGS of ornithorhynchus anatinus"] - name: entrezdirect esummary test_entrezdirect_esummary_genome - command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/esummary/nextflow.config tags: - entrezdirect - entrezdirect/esummary @@ -17,7 +17,7 @@ contains: ["Hypsibius dujardini"] - name: entrezdirect esummary test_entrezdirect_esummary_assembly - command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/esummary/nextflow.config tags: - entrezdirect - entrezdirect/esummary diff --git a/tests/modules/nf-core/entrezdirect/xtract/test.yml b/tests/modules/nf-core/entrezdirect/xtract/test.yml index a4b506168e3..58f60d21b81 100644 --- a/tests/modules/nf-core/entrezdirect/xtract/test.yml +++ b/tests/modules/nf-core/entrezdirect/xtract/test.yml @@ -1,5 +1,5 @@ - name: entrezdirect xtract test_entrezdirect_xtract_assembly - command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/xtract/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/xtract -entry test_entrezdirect_xtract_assembly -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/xtract/nextflow.config tags: - entrezdirect - entrezdirect/xtract @@ -8,7 +8,7 @@ md5sum: 17073db7c14890aef30f5e3f2d003d32 - name: entrezdirect xtract test_entrezdirect_xtract_genome - command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/xtract/nextflow.config + command: nextflow run ./tests/modules/nf-core/entrezdirect/xtract -entry test_entrezdirect_xtract_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/entrezdirect/xtract/nextflow.config tags: - entrezdirect - entrezdirect/xtract diff --git a/tests/modules/nf-core/epang/test.yml b/tests/modules/nf-core/epang/test.yml index b4b861c1a96..c7048570984 100644 --- a/tests/modules/nf-core/epang/test.yml +++ b/tests/modules/nf-core/epang/test.yml @@ -1,5 +1,5 @@ - name: epang test_epang - command: nextflow run ./tests/modules/epang -entry test_epang -c ./tests/config/nextflow.config -c ./tests/modules/epang/nextflow.config + command: nextflow run ./tests/modules/nf-core/epang -entry test_epang -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/epang/nextflow.config tags: - epang files: diff --git a/tests/modules/nf-core/expansionhunter/test.yml b/tests/modules/nf-core/expansionhunter/test.yml index f9282f8c4c9..0f49183590e 100644 --- a/tests/modules/nf-core/expansionhunter/test.yml +++ b/tests/modules/nf-core/expansionhunter/test.yml @@ -1,5 +1,5 @@ - name: expansionhunter test_expansionhunter - command: nextflow run ./tests/modules/expansionhunter -entry test_expansionhunter -c ./tests/config/nextflow.config -c ./tests/modules/expansionhunter/nextflow.config + command: nextflow run ./tests/modules/nf-core/expansionhunter -entry test_expansionhunter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/expansionhunter/nextflow.config tags: - expansionhunter files: diff --git a/tests/modules/nf-core/faqcs/test.yml b/tests/modules/nf-core/faqcs/test.yml index ef50d30d145..43023a8937f 100644 --- a/tests/modules/nf-core/faqcs/test.yml +++ b/tests/modules/nf-core/faqcs/test.yml @@ -1,5 +1,5 @@ - name: faqcs test_fastp_single_end - command: nextflow run tests/modules/faqcs -entry test_fastp_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_single_end -c tests/config/nextflow.config tags: - faqcs files: @@ -26,7 +26,7 @@ md5sum: 2a38d7e7ab5299336e9669c393c9da6c - name: faqcs test_fastp_paired_end - command: nextflow run tests/modules/faqcs -entry test_fastp_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_paired_end -c tests/config/nextflow.config tags: - faqcs files: diff --git a/tests/modules/nf-core/fargene/test.yml b/tests/modules/nf-core/fargene/test.yml index 3ca94bc0715..9801d63a28d 100644 --- a/tests/modules/nf-core/fargene/test.yml +++ b/tests/modules/nf-core/fargene/test.yml @@ -1,5 +1,5 @@ - name: fargene - command: nextflow run ./tests/modules/fargene -entry test_fargene -c ./tests/config/nextflow.config -c ./tests/modules/fargene/nextflow.config + command: nextflow run ./tests/modules/nf-core/fargene -entry test_fargene -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fargene/nextflow.config tags: - fargene files: diff --git a/tests/modules/nf-core/fastani/test.yml b/tests/modules/nf-core/fastani/test.yml index f3748d2548c..2ac0adc0949 100644 --- a/tests/modules/nf-core/fastani/test.yml +++ b/tests/modules/nf-core/fastani/test.yml @@ -1,5 +1,5 @@ - name: fastani - command: nextflow run ./tests/modules/fastani -entry test_fastani -c ./tests/config/nextflow.config -c ./tests/modules/fastani/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastani -entry test_fastani -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastani/nextflow.config tags: - fastani files: diff --git a/tests/modules/nf-core/fastawindows/test.yml b/tests/modules/nf-core/fastawindows/test.yml index 5cdd0e2c250..677dc8ca66f 100644 --- a/tests/modules/nf-core/fastawindows/test.yml +++ b/tests/modules/nf-core/fastawindows/test.yml @@ -1,5 +1,5 @@ - name: fastawindows test_fastawindows - command: nextflow run ./tests/modules/fastawindows -entry test_fastawindows -c ./tests/config/nextflow.config -c ./tests/modules/fastawindows/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastawindows -entry test_fastawindows -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastawindows/nextflow.config tags: - fastawindows files: diff --git a/tests/modules/nf-core/fastk/fastk/test.yml b/tests/modules/nf-core/fastk/fastk/test.yml index fd3fdebef48..fa075ca7f76 100644 --- a/tests/modules/nf-core/fastk/fastk/test.yml +++ b/tests/modules/nf-core/fastk/fastk/test.yml @@ -1,5 +1,5 @@ - name: fastk fastk test_fastk_fastk_single_end - command: nextflow run ./tests/modules/fastk/fastk -entry test_fastk_fastk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastk/fastk/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastk/fastk -entry test_fastk_fastk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastk/fastk/nextflow.config tags: - fastk - fastk/fastk @@ -20,7 +20,7 @@ md5sum: 43d426c95d277b8148406624d513bd40 - name: fastk fastk test_fastk_fastk_paired_end - command: nextflow run ./tests/modules/fastk/fastk -entry test_fastk_fastk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastk/fastk/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastk/fastk -entry test_fastk_fastk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastk/fastk/nextflow.config tags: - fastk - fastk/fastk diff --git a/tests/modules/nf-core/fastk/histex/test.yml b/tests/modules/nf-core/fastk/histex/test.yml index 8348af8fbf9..df8e0d914e5 100644 --- a/tests/modules/nf-core/fastk/histex/test.yml +++ b/tests/modules/nf-core/fastk/histex/test.yml @@ -1,5 +1,5 @@ - name: fastk histex test_fastk_histex - command: nextflow run ./tests/modules/fastk/histex -entry test_fastk_histex -c ./tests/config/nextflow.config -c ./tests/modules/fastk/histex/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastk/histex -entry test_fastk_histex -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastk/histex/nextflow.config tags: - fastk/histex - fastk diff --git a/tests/modules/nf-core/fastk/merge/test.yml b/tests/modules/nf-core/fastk/merge/test.yml index 2c3fba2e72b..d8fe5ccc666 100644 --- a/tests/modules/nf-core/fastk/merge/test.yml +++ b/tests/modules/nf-core/fastk/merge/test.yml @@ -1,5 +1,5 @@ - name: fastk merge test_fastk_merge_hist_only - command: nextflow run ./tests/modules/fastk/merge -entry test_fastk_merge_hist_only -c ./tests/config/nextflow.config -c ./tests/modules/fastk/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastk/merge -entry test_fastk_merge_hist_only -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastk/merge/nextflow.config tags: - fastk/merge - fastk @@ -14,7 +14,7 @@ md5sum: 7d882f4e3542df1a2f5cb0858b12dc03 - name: fastk merge test_fastk_merge_all_files - command: nextflow run ./tests/modules/fastk/merge -entry test_fastk_merge_all_files -c ./tests/config/nextflow.config -c ./tests/modules/fastk/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastk/merge -entry test_fastk_merge_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastk/merge/nextflow.config tags: - fastk/merge - fastk diff --git a/tests/modules/nf-core/fastp/test.yml b/tests/modules/nf-core/fastp/test.yml index d64b5506a2f..c8e93ad7f9a 100644 --- a/tests/modules/nf-core/fastp/test.yml +++ b/tests/modules/nf-core/fastp/test.yml @@ -1,5 +1,5 @@ - name: fastp test_fastp_single_end - command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config tags: - fastp files: @@ -23,7 +23,7 @@ - "reads passed filter: 99" - name: fastp test_fastp_paired_end - command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config + command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config tags: - fastp files: @@ -56,7 +56,7 @@ - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<test1" - name: seqtk rename test_seqtk_rename_fq - command: nextflow run tests/modules/seqtk/rename -entry test_seqtk_rename_fq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename_fq -c tests/config/nextflow.config tags: - seqtk - seqtk/rename diff --git a/tests/modules/nf-core/seqtk/sample/test.yml b/tests/modules/nf-core/seqtk/sample/test.yml index 2a677e0ad6a..1f847ebe9c0 100644 --- a/tests/modules/nf-core/seqtk/sample/test.yml +++ b/tests/modules/nf-core/seqtk/sample/test.yml @@ -1,5 +1,5 @@ - name: seqtk sample test_seqtk_sample_single_end - command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_single_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/sample -entry test_seqtk_sample_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/sample/nextflow.config tags: - seqtk - seqtk/sample @@ -9,7 +9,7 @@ - "@ERR5069949" - name: seqtk sample test_seqtk_sample_paired_end - command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/sample -entry test_seqtk_sample_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/sample/nextflow.config tags: - seqtk - seqtk/sample diff --git a/tests/modules/nf-core/seqtk/seq/test.yml b/tests/modules/nf-core/seqtk/seq/test.yml index 0d709c57d31..1d0e3286232 100644 --- a/tests/modules/nf-core/seqtk/seq/test.yml +++ b/tests/modules/nf-core/seqtk/seq/test.yml @@ -1,5 +1,5 @@ - name: seqtk seq test_seqtk_seq - command: nextflow run tests/modules/seqtk/seq -entry test_seqtk_seq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq -c tests/config/nextflow.config tags: - seqtk/seq - seqtk @@ -8,7 +8,7 @@ md5sum: 50d73992c8c7e56dc095ef47ec52a754 - name: seqtk seq test_seqtk_seq_fq - command: nextflow run tests/modules/seqtk/seq -entry test_seqtk_seq_fq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq_fq -c tests/config/nextflow.config tags: - seqtk/seq - seqtk diff --git a/tests/modules/nf-core/seqtk/subseq/test.yml b/tests/modules/nf-core/seqtk/subseq/test.yml index 4003e3ab89c..9b9e0750647 100644 --- a/tests/modules/nf-core/seqtk/subseq/test.yml +++ b/tests/modules/nf-core/seqtk/subseq/test.yml @@ -1,5 +1,5 @@ - name: seqtk subseq test_seqtk_subseq - command: nextflow run ./tests/modules/seqtk/subseq -entry test_seqtk_subseq -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/subseq/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/subseq -entry test_seqtk_subseq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqtk/subseq/nextflow.config tags: - seqtk - seqtk/subseq diff --git a/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml b/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml index f3ea6cf0ba2..3326aef5ff8 100644 --- a/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml +++ b/tests/modules/nf-core/sequenzautils/bam2seqz/test.yml @@ -1,5 +1,5 @@ - name: sequenzautils bam2seqz - command: nextflow run ./tests/modules/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c ./tests/config/nextflow.config -c ./tests/modules/sequenzautils/bam2seqz/nextflow.config + command: nextflow run ./tests/modules/nf-core/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sequenzautils/bam2seqz/nextflow.config tags: - sequenzautils - sequenzautils/bam2seqz diff --git a/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml b/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml index 21ddc4ab0ef..973adb44fe1 100644 --- a/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml +++ b/tests/modules/nf-core/sequenzautils/gcwiggle/test.yml @@ -1,5 +1,5 @@ - name: sequenzautils gcwiggle - command: nextflow run ./tests/modules/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c ./tests/config/nextflow.config -c ./tests/modules/sequenzautils/gcwiggle/nextflow.config + command: nextflow run ./tests/modules/nf-core/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sequenzautils/gcwiggle/nextflow.config tags: - sequenzautils - sequenzautils/gcwiggle diff --git a/tests/modules/nf-core/seqwish/induce/test.yml b/tests/modules/nf-core/seqwish/induce/test.yml index 8a700f3e8af..20d17b794de 100644 --- a/tests/modules/nf-core/seqwish/induce/test.yml +++ b/tests/modules/nf-core/seqwish/induce/test.yml @@ -1,5 +1,5 @@ - name: seqwish induce transcriptome - command: nextflow run ./tests/modules/seqwish/induce -entry test_seqwish_induce_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/seqwish/induce/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqwish/induce -entry test_seqwish_induce_transcriptome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqwish/induce/nextflow.config tags: - seqwish - seqwish/induce @@ -8,7 +8,7 @@ md5sum: 216a02d3aca322a457c31a62c628548e - name: seqwish induce pangenome - command: nextflow run ./tests/modules/seqwish/induce -entry test_seqwish_induce_pangenome -c ./tests/config/nextflow.config -c ./tests/modules/seqwish/induce/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqwish/induce -entry test_seqwish_induce_pangenome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seqwish/induce/nextflow.config tags: - seqwish - seqwish/induce diff --git a/tests/modules/nf-core/seroba/run/test.yml b/tests/modules/nf-core/seroba/run/test.yml index 2aa6f81488e..adcc2a2e571 100644 --- a/tests/modules/nf-core/seroba/run/test.yml +++ b/tests/modules/nf-core/seroba/run/test.yml @@ -1,5 +1,5 @@ - name: seroba run test_seroba_run - command: nextflow run ./tests/modules/seroba/run -entry test_seroba_run -c ./tests/config/nextflow.config -c ./tests/modules/seroba/run/nextflow.config + command: nextflow run ./tests/modules/nf-core/seroba/run -entry test_seroba_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/seroba/run/nextflow.config tags: - seroba - seroba/run diff --git a/tests/modules/nf-core/sexdeterrmine/test.yml b/tests/modules/nf-core/sexdeterrmine/test.yml index bb3f701ed3f..73b98aed524 100644 --- a/tests/modules/nf-core/sexdeterrmine/test.yml +++ b/tests/modules/nf-core/sexdeterrmine/test.yml @@ -1,5 +1,5 @@ - name: sexdeterrmine test_sexdeterrmine - command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config tags: - sexdeterrmine files: diff --git a/tests/modules/nf-core/shasta/test.yml b/tests/modules/nf-core/shasta/test.yml index 9b9b054caf6..356b0194ff6 100644 --- a/tests/modules/nf-core/shasta/test.yml +++ b/tests/modules/nf-core/shasta/test.yml @@ -1,5 +1,5 @@ - name: shasta test_shasta - command: nextflow run ./tests/modules/shasta -entry test_shasta -c ./tests/config/nextflow.config -c ./tests/modules/shasta/nextflow.config + command: nextflow run ./tests/modules/nf-core/shasta -entry test_shasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shasta/nextflow.config tags: - shasta files: diff --git a/tests/modules/nf-core/shasum/test.yml b/tests/modules/nf-core/shasum/test.yml index 6778d156049..eab267eabcd 100644 --- a/tests/modules/nf-core/shasum/test.yml +++ b/tests/modules/nf-core/shasum/test.yml @@ -1,5 +1,5 @@ - name: shasum test_shasum - command: nextflow run tests/modules/shasum -entry test_shasum -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/shasum -entry test_shasum -c tests/config/nextflow.config tags: - shasum files: diff --git a/tests/modules/nf-core/shigatyper/test.yml b/tests/modules/nf-core/shigatyper/test.yml index 9dda573be42..8b6ea1a0e2e 100644 --- a/tests/modules/nf-core/shigatyper/test.yml +++ b/tests/modules/nf-core/shigatyper/test.yml @@ -1,5 +1,5 @@ - name: shigatyper test_shigatyper_pe - command: nextflow run tests/modules/shigatyper -entry test_shigatyper_pe -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_pe -c tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config tags: - shigatyper files: @@ -9,7 +9,7 @@ md5sum: d8ca45ed88dfba9bc570c01e4b49773b - name: shigatyper test_shigatyper_se - command: nextflow run tests/modules/shigatyper -entry test_shigatyper_se -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_se -c tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config tags: - shigatyper files: @@ -19,7 +19,7 @@ md5sum: 8bbf165da5a5df3b7771a33aad197eec - name: shigatyper test_shigatyper_ont - command: nextflow run tests/modules/shigatyper -entry test_shigatyper_ont -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_ont -c tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config tags: - shigatyper files: diff --git a/tests/modules/nf-core/shovill/test.yml b/tests/modules/nf-core/shovill/test.yml index 6fdd2f3f3ad..755c384fb0e 100644 --- a/tests/modules/nf-core/shovill/test.yml +++ b/tests/modules/nf-core/shovill/test.yml @@ -1,5 +1,5 @@ - name: shovill with spades - command: nextflow run ./tests/modules/shovill -entry test_shovill -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config + command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config tags: - shovill files: @@ -13,7 +13,7 @@ - path: output/shovill/shovill.log - name: shovill with megahit - command: nextflow run ./tests/modules/shovill -entry test_shovill_megahit -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config + command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill_megahit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config tags: - shovill files: @@ -26,7 +26,7 @@ - path: output/shovill/shovill.log - name: shovill with skesa - command: nextflow run ./tests/modules/shovill -entry test_shovill_skesa -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config + command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill_skesa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config tags: - shovill files: @@ -39,7 +39,7 @@ - path: output/shovill/shovill.log - name: shovill with velvet - command: nextflow run ./tests/modules/shovill -entry test_shovill_velvet -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config + command: nextflow run ./tests/modules/nf-core/shovill -entry test_shovill_velvet -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shovill/nextflow.config tags: - shovill files: diff --git a/tests/modules/nf-core/sistr/test.yml b/tests/modules/nf-core/sistr/test.yml index 88182f28c98..2012d84ea18 100644 --- a/tests/modules/nf-core/sistr/test.yml +++ b/tests/modules/nf-core/sistr/test.yml @@ -1,5 +1,5 @@ - name: sistr test_sistr - command: nextflow run tests/modules/sistr -entry test_sistr -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/sistr -entry test_sistr -c tests/config/nextflow.config tags: - sistr files: diff --git a/tests/modules/nf-core/slimfastq/test.yml b/tests/modules/nf-core/slimfastq/test.yml index f0d8b446a65..c008ec2219e 100644 --- a/tests/modules/nf-core/slimfastq/test.yml +++ b/tests/modules/nf-core/slimfastq/test.yml @@ -1,5 +1,5 @@ - name: slimfastq test_slimfastq_single_end - command: nextflow run tests/modules/slimfastq -entry test_slimfastq_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_single_end -c tests/config/nextflow.config tags: - slimfastq files: @@ -9,7 +9,7 @@ md5sum: f52351f5c9e6259af02745c8eae5c780 - name: slimfastq test_slimfastq_paired_end - command: nextflow run tests/modules/slimfastq -entry test_slimfastq_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_paired_end -c tests/config/nextflow.config tags: - slimfastq files: @@ -21,7 +21,7 @@ md5sum: 6239853705877651a4851c4cb6d62da4 - name: slimfastq test_slimfastq_nanopore - command: nextflow run tests/modules/slimfastq -entry test_slimfastq_nanopore -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_nanopore -c tests/config/nextflow.config tags: - slimfastq files: @@ -31,7 +31,7 @@ md5sum: 33153f1103482a2bd35cb2f4c337c5e8 - name: slimfastq test_slimfastq_pacbio - command: nextflow run tests/modules/slimfastq -entry test_slimfastq_pacbio -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_pacbio -c tests/config/nextflow.config tags: - slimfastq files: diff --git a/tests/modules/nf-core/snapaligner/align/test.yml b/tests/modules/nf-core/snapaligner/align/test.yml index b7e63f10251..1acf9af5985 100644 --- a/tests/modules/nf-core/snapaligner/align/test.yml +++ b/tests/modules/nf-core/snapaligner/align/test.yml @@ -1,5 +1,5 @@ - name: snapaligner align test_snapaligner_single - command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_single -c ./tests/config/nextflow.config -c ./tests/modules/snapaligner/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/snapaligner/align -entry test_snapaligner_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snapaligner/align/nextflow.config tags: - snapaligner/align - snapaligner @@ -10,7 +10,7 @@ md5sum: f180c68a77445b317a22e3f1d6e6e114 - name: snapaligner align test_snapaligner_paired - command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config -c ./tests/modules/snapaligner/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snapaligner/align/nextflow.config tags: - snapaligner/align - snapaligner diff --git a/tests/modules/nf-core/snapaligner/index/test.yml b/tests/modules/nf-core/snapaligner/index/test.yml index 2c4b49351c9..bdb6871f31c 100644 --- a/tests/modules/nf-core/snapaligner/index/test.yml +++ b/tests/modules/nf-core/snapaligner/index/test.yml @@ -1,5 +1,5 @@ - name: snapaligner index test_snapaligner_index - command: nextflow run tests/modules/snapaligner/index -entry test_snapaligner_index -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snapaligner/index -entry test_snapaligner_index -c tests/config/nextflow.config tags: - snapaligner/index - snapaligner diff --git a/tests/modules/nf-core/snippy/core/test.yml b/tests/modules/nf-core/snippy/core/test.yml index 792dc3dc3da..d6147d9fe2f 100644 --- a/tests/modules/nf-core/snippy/core/test.yml +++ b/tests/modules/nf-core/snippy/core/test.yml @@ -1,5 +1,5 @@ - name: snippy core test_snippy_core - command: nextflow run ./tests/modules/snippy/core -entry test_snippy_core -c ./tests/config/nextflow.config -c ./tests/modules/snippy/core/nextflow.config + command: nextflow run ./tests/modules/nf-core/snippy/core -entry test_snippy_core -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snippy/core/nextflow.config tags: - snippy - snippy/core diff --git a/tests/modules/nf-core/snippy/run/test.yml b/tests/modules/nf-core/snippy/run/test.yml index 10e24f558d5..2bca969affb 100644 --- a/tests/modules/nf-core/snippy/run/test.yml +++ b/tests/modules/nf-core/snippy/run/test.yml @@ -1,6 +1,6 @@ - name: snippy run test_snippy_run command: | - nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config + nextflow run ./tests/modules/nf-core/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c ./tests/modules/nf-core/snippy/run/nextflow.config tags: - snippy/run - snippy diff --git a/tests/modules/nf-core/snpdists/test.yml b/tests/modules/nf-core/snpdists/test.yml index c23945ce170..784abb6a7f2 100644 --- a/tests/modules/nf-core/snpdists/test.yml +++ b/tests/modules/nf-core/snpdists/test.yml @@ -1,5 +1,5 @@ - name: snpdists - command: nextflow run ./tests/modules/snpdists -entry test_snpdists -c ./tests/config/nextflow.config -c ./tests/modules/snpdists/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpdists -entry test_snpdists -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snpdists/nextflow.config tags: - snpdists files: diff --git a/tests/modules/nf-core/snpeff/test.yml b/tests/modules/nf-core/snpeff/test.yml index b7d3c7a42d2..b2043ba032e 100644 --- a/tests/modules/nf-core/snpeff/test.yml +++ b/tests/modules/nf-core/snpeff/test.yml @@ -1,5 +1,5 @@ - name: snpeff test_snpeff - command: nextflow run ./tests/modules/snpeff -entry test_snpeff -c ./tests/config/nextflow.config -c ./tests/modules/snpeff/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpeff -entry test_snpeff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snpeff/nextflow.config tags: - snpeff files: diff --git a/tests/modules/nf-core/snpsift/split/test.yml b/tests/modules/nf-core/snpsift/split/test.yml index 529fbca59a5..78e5cb99607 100644 --- a/tests/modules/nf-core/snpsift/split/test.yml +++ b/tests/modules/nf-core/snpsift/split/test.yml @@ -1,5 +1,5 @@ - name: snpsift split test_snpsift_split_base - command: nextflow run tests/modules/snpsift/split -entry test_snpsift_split_base -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_base -c tests/config/nextflow.config tags: - snpsift/split - snpsift @@ -10,7 +10,7 @@ md5sum: 2b9f6b788db6c4fcbf258db763d8fab7 - name: snpsift split test_snpsift_split_gz - command: nextflow run tests/modules/snpsift/split -entry test_snpsift_split_gz -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_gz -c tests/config/nextflow.config tags: - snpsift/split - snpsift @@ -21,7 +21,7 @@ md5sum: 6bd63376670d6c1445caea2f31a3f579 - name: snpsift split test_snpsift_join - command: nextflow run tests/modules/snpsift/split -entry test_snpsift_join -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_join -c tests/config/nextflow.config tags: - snpsift/split - snpsift diff --git a/tests/modules/nf-core/snpsites/test.yml b/tests/modules/nf-core/snpsites/test.yml index 9d80dd514bf..e8e071e499f 100644 --- a/tests/modules/nf-core/snpsites/test.yml +++ b/tests/modules/nf-core/snpsites/test.yml @@ -1,5 +1,5 @@ - name: snpsites - command: nextflow run ./tests/modules/snpsites -entry test_snpsites -c ./tests/config/nextflow.config -c ./tests/modules/snpsites/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsites -entry test_snpsites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snpsites/nextflow.config tags: - snpsites files: diff --git a/tests/modules/nf-core/somalier/extract/test.yml b/tests/modules/nf-core/somalier/extract/test.yml index 356b2c7fc45..23c6861866d 100644 --- a/tests/modules/nf-core/somalier/extract/test.yml +++ b/tests/modules/nf-core/somalier/extract/test.yml @@ -1,5 +1,5 @@ - name: somalier extract test_somalier_extract - command: nextflow run ./tests/modules/somalier/extract/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/extract/nextflow.config -entry test_somalier_extract + command: nextflow run ./tests/modules/nf-core/somalier/extract/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/somalier/extract/nextflow.config -entry test_somalier_extract tags: - somalier/extract - somalier diff --git a/tests/modules/nf-core/somalier/relate/test.yml b/tests/modules/nf-core/somalier/relate/test.yml index b2e886ef649..604a4e3ba17 100644 --- a/tests/modules/nf-core/somalier/relate/test.yml +++ b/tests/modules/nf-core/somalier/relate/test.yml @@ -1,5 +1,5 @@ - name: somalier relate test_somalier_relate - command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate + command: nextflow run ./tests/modules/nf-core/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/somalier/relate/nextflow.config -entry test_somalier_relate tags: - somalier/relate - somalier @@ -12,7 +12,7 @@ md5sum: 97257d88886db1325c4d7d10cefa7169 - name: somalier relate test_somalier_relate_ped_groups - command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate_ped_groups + command: nextflow run ./tests/modules/nf-core/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/somalier/relate/nextflow.config -entry test_somalier_relate_ped_groups tags: - somalier/relate - somalier diff --git a/tests/modules/nf-core/sourmash/sketch/test.yml b/tests/modules/nf-core/sourmash/sketch/test.yml index 5bd18967f5b..be113397987 100644 --- a/tests/modules/nf-core/sourmash/sketch/test.yml +++ b/tests/modules/nf-core/sourmash/sketch/test.yml @@ -1,5 +1,5 @@ - name: sourmash sketch test_sourmash_sketch - command: nextflow run tests/modules/sourmash/sketch -entry test_sourmash_sketch -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/sourmash/sketch -entry test_sourmash_sketch -c tests/config/nextflow.config tags: - sourmash - sourmash/sketch diff --git a/tests/modules/nf-core/spades/test.yml b/tests/modules/nf-core/spades/test.yml index d016c1a0181..b4850b50b0f 100644 --- a/tests/modules/nf-core/spades/test.yml +++ b/tests/modules/nf-core/spades/test.yml @@ -1,5 +1,5 @@ - name: spades test_spades_single_end - command: nextflow run ./tests/modules/spades -entry test_spades_single_end -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config + command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config tags: - spades files: @@ -12,7 +12,7 @@ - path: output/spades/test.spades.log - name: spades test_spades_paired_end - command: nextflow run ./tests/modules/spades -entry test_spades_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config + command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config tags: - spades files: @@ -24,7 +24,7 @@ - path: output/spades/warnings.log - name: spades test_spades_illumina_nanopore - command: nextflow run ./tests/modules/spades -entry test_spades_illumina_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config + command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_illumina_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config tags: - spades files: @@ -38,7 +38,7 @@ - path: output/spades/warnings.log - name: spades test_spades_illumina_pacbio - command: nextflow run ./tests/modules/spades -entry test_spades_illumina_pacbio -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config + command: nextflow run ./tests/modules/nf-core/spades -entry test_spades_illumina_pacbio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spades/nextflow.config tags: - spades files: diff --git a/tests/modules/nf-core/spatyper/test.yml b/tests/modules/nf-core/spatyper/test.yml index 6e1f814456a..4b998739a6e 100644 --- a/tests/modules/nf-core/spatyper/test.yml +++ b/tests/modules/nf-core/spatyper/test.yml @@ -1,5 +1,5 @@ - name: spatyper test_spatyper - command: nextflow run ./tests/modules/spatyper -entry test_spatyper -c ./tests/config/nextflow.config -c ./tests/modules/spatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/spatyper -entry test_spatyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spatyper/nextflow.config tags: - spatyper files: @@ -7,7 +7,7 @@ md5sum: a698352823875171696e5e7ed7015c13 - name: spatyper test_spatyper_enrich - command: nextflow run ./tests/modules/spatyper -entry test_spatyper_enrich -c ./tests/config/nextflow.config -c ./tests/modules/spatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/spatyper -entry test_spatyper_enrich -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spatyper/nextflow.config tags: - spatyper files: diff --git a/tests/modules/nf-core/sratools/fasterqdump/test.yml b/tests/modules/nf-core/sratools/fasterqdump/test.yml index 6fbf608cc49..dcccb204b2d 100644 --- a/tests/modules/nf-core/sratools/fasterqdump/test.yml +++ b/tests/modules/nf-core/sratools/fasterqdump/test.yml @@ -1,5 +1,5 @@ - name: sratools fasterqdump test_sratools_fasterqdump_single_end - command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config + command: nextflow run ./tests/modules/nf-core/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sratools/fasterqdump/nextflow.config tags: - sratools - sratools/fasterqdump @@ -13,7 +13,7 @@ - "sratools: 2.11.0" - name: sratools fasterqdump test_sratools_fasterqdump_paired_end - command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config + command: nextflow run ./tests/modules/nf-core/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sratools/fasterqdump/nextflow.config tags: - sratools - sratools/fasterqdump diff --git a/tests/modules/nf-core/sratools/prefetch/test.yml b/tests/modules/nf-core/sratools/prefetch/test.yml index a6c213f8a59..538b30a166e 100644 --- a/tests/modules/nf-core/sratools/prefetch/test.yml +++ b/tests/modules/nf-core/sratools/prefetch/test.yml @@ -1,5 +1,5 @@ - name: sratools prefetch test_sratools_prefetch - command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config + command: nextflow run ./tests/modules/nf-core/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sratools/prefetch/nextflow.config tags: - sratools/prefetch - sratools diff --git a/tests/modules/nf-core/srst2/srst2/test.yml b/tests/modules/nf-core/srst2/srst2/test.yml index f7621f4f812..6d70b5b4e7b 100644 --- a/tests/modules/nf-core/srst2/srst2/test.yml +++ b/tests/modules/nf-core/srst2/srst2/test.yml @@ -1,12 +1,12 @@ - name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db - command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config tags: - srst2/srst2 - srst2 exit_code: 1 - name: srst2 srst2 test_srst2_srst2_mlst - command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config tags: - srst2/srst2 - srst2 @@ -21,7 +21,7 @@ md5sum: a0c256a2fd3636069710b8ef22ee5ea7 - name: srst2 srst2 test_srst2_srst2_paired_end - command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config tags: - srst2/srst2 - srst2 @@ -35,7 +35,7 @@ md5sum: b446a70f1a2b4f60757829bcd744a214 - name: srst2 srst2 test_srst2_srst2_single_end - command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config tags: - srst2/srst2 - srst2 diff --git a/tests/modules/nf-core/ssuissero/test.yml b/tests/modules/nf-core/ssuissero/test.yml index ff61b2679ae..a2aaf250e4c 100644 --- a/tests/modules/nf-core/ssuissero/test.yml +++ b/tests/modules/nf-core/ssuissero/test.yml @@ -1,5 +1,5 @@ - name: ssuissero test_ssuissero - command: nextflow run tests/modules/ssuissero -entry test_ssuissero -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ssuissero -entry test_ssuissero -c tests/config/nextflow.config tags: - ssuissero files: diff --git a/tests/modules/nf-core/stadeniolib/scramble/test.yml b/tests/modules/nf-core/stadeniolib/scramble/test.yml index cea6fb702e4..e7064d946af 100644 --- a/tests/modules/nf-core/stadeniolib/scramble/test.yml +++ b/tests/modules/nf-core/stadeniolib/scramble/test.yml @@ -1,5 +1,5 @@ - name: stadeniolib test_stadeniolib - command: nextflow run tests/modules/stadeniolib -entry test_stadeniolib -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/stadeniolib -entry test_stadeniolib -c tests/config/nextflow.config tags: - stadeniolib files: diff --git a/tests/modules/nf-core/staphopiasccmec/test.yml b/tests/modules/nf-core/staphopiasccmec/test.yml index ac3f66da300..332138a09af 100644 --- a/tests/modules/nf-core/staphopiasccmec/test.yml +++ b/tests/modules/nf-core/staphopiasccmec/test.yml @@ -1,5 +1,5 @@ - name: staphopiasccmec test_staphopiasccmec - command: nextflow run ./tests/modules/staphopiasccmec -entry test_staphopiasccmec -c ./tests/config/nextflow.config -c ./tests/modules/staphopiasccmec/nextflow.config + command: nextflow run ./tests/modules/nf-core/staphopiasccmec -entry test_staphopiasccmec -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/staphopiasccmec/nextflow.config tags: - staphopiasccmec files: @@ -7,7 +7,7 @@ md5sum: e6460d4164f3af5b290c5ccdb11343bf - name: staphopiasccmec test_staphopiasccmec_hamming - command: nextflow run ./tests/modules/staphopiasccmec -entry test_staphopiasccmec_hamming -c ./tests/config/nextflow.config -c ./tests/modules/staphopiasccmec/nextflow.config + command: nextflow run ./tests/modules/nf-core/staphopiasccmec -entry test_staphopiasccmec_hamming -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/staphopiasccmec/nextflow.config tags: - staphopiasccmec files: diff --git a/tests/modules/nf-core/star/align/test.yml b/tests/modules/nf-core/star/align/test.yml index b75802954e8..a90c903941e 100644 --- a/tests/modules/nf-core/star/align/test.yml +++ b/tests/modules/nf-core/star/align/test.yml @@ -1,5 +1,5 @@ - name: star align test_star_alignment_single_end - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config tags: - star/align - star @@ -43,7 +43,7 @@ - path: output/star/test.SJ.out.tab - name: star align test_star_alignment_paired_end - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config tags: - star/align - star @@ -87,7 +87,7 @@ - path: output/star/test.SJ.out.tab - name: star align test_star_alignment_paired_end_for_fusion - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_paired_end_for_fusion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config tags: - star/align - star @@ -131,7 +131,7 @@ - path: output/star/test.SJ.out.tab - name: star align test_star_alignment_paired_end_for_starfusion - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_starfusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_paired_end_for_starfusion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config tags: - star/align - star @@ -177,7 +177,7 @@ - path: output/star/test.SJ.out.tab - name: star align test_star_alignment_single_end stub - command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/align/nextflow.config -stub-run tags: - star/align - star diff --git a/tests/modules/nf-core/star/genomegenerate/test.yml b/tests/modules/nf-core/star/genomegenerate/test.yml index d980764ca2a..55fd4999970 100644 --- a/tests/modules/nf-core/star/genomegenerate/test.yml +++ b/tests/modules/nf-core/star/genomegenerate/test.yml @@ -1,5 +1,5 @@ - name: star genomegenerate test_star_genomegenerate - command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config + command: nextflow run ./tests/modules/nf-core/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/genomegenerate/nextflow.config tags: - star - star/genomegenerate @@ -37,7 +37,7 @@ md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - name: star genomegenerate test_star_genomegenerate stub - command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/star/genomegenerate/nextflow.config -stub-run tags: - star - star/genomegenerate diff --git a/tests/modules/nf-core/stranger/test.yml b/tests/modules/nf-core/stranger/test.yml index bf922c86a40..b68c867d009 100644 --- a/tests/modules/nf-core/stranger/test.yml +++ b/tests/modules/nf-core/stranger/test.yml @@ -1,5 +1,5 @@ - name: stranger test_stranger - command: nextflow run tests/modules/stranger -entry test_stranger -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger -c tests/config/nextflow.config tags: - stranger files: @@ -13,7 +13,7 @@ md5sum: 5ec35fd835fb1be50bc3e7c004310fc0 - name: stranger test_stranger_without_optional_variant_catalog - command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config tags: - stranger files: @@ -27,7 +27,7 @@ md5sum: 8558542a007e90ea5dcdceed3f12585d - name: stranger test_stranger_without_optional_variant_catalog_stubs - command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run tags: - stranger files: diff --git a/tests/modules/nf-core/strelka/germline/test.yml b/tests/modules/nf-core/strelka/germline/test.yml index 8db81aa06ea..989ff3e8d77 100644 --- a/tests/modules/nf-core/strelka/germline/test.yml +++ b/tests/modules/nf-core/strelka/germline/test.yml @@ -1,5 +1,5 @@ - name: strelka germline test_strelka_germline - command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline -c ./tests/config/nextflow.config -c ./tests/modules/strelka/germline/nextflow.config + command: nextflow run ./tests/modules/nf-core/strelka/germline -entry test_strelka_germline -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/germline/nextflow.config tags: - strelka - strelka/germline @@ -10,7 +10,7 @@ - path: output/strelka/test.variants.vcf.gz.tbi - name: strelka germline test_strelka_germline_target_bed - command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/strelka/germline/nextflow.config + command: nextflow run ./tests/modules/nf-core/strelka/germline -entry test_strelka_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/germline/nextflow.config tags: - strelka - strelka/germline diff --git a/tests/modules/nf-core/strelka/somatic/test.yml b/tests/modules/nf-core/strelka/somatic/test.yml index 787f3b19dcc..07e5306f02d 100644 --- a/tests/modules/nf-core/strelka/somatic/test.yml +++ b/tests/modules/nf-core/strelka/somatic/test.yml @@ -1,5 +1,5 @@ - name: strelka somatic test_strelka_somatic - command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config + command: nextflow run ./tests/modules/nf-core/strelka/somatic -entry test_strelka_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/somatic/nextflow.config tags: - strelka - strelka/somatic @@ -10,7 +10,7 @@ - path: output/strelka/test.somatic_snvs.vcf.gz.tbi - name: strelka somatic test_strelka_best_practices_somatic - command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config + command: nextflow run ./tests/modules/nf-core/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/strelka/somatic/nextflow.config tags: - strelka - strelka/somatic diff --git a/tests/modules/nf-core/stringtie/merge/test.yml b/tests/modules/nf-core/stringtie/merge/test.yml index fb25bf63fa9..89e0a90a350 100644 --- a/tests/modules/nf-core/stringtie/merge/test.yml +++ b/tests/modules/nf-core/stringtie/merge/test.yml @@ -1,5 +1,5 @@ - name: stringtie merge forward-strand - command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config tags: - stringtie - stringtie/merge @@ -23,7 +23,7 @@ md5sum: a914bd55b68a4b5f607738b17861e362 - name: stringtie merge test_stringtie_reverse_merge - command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config tags: - stringtie - stringtie/merge @@ -47,7 +47,7 @@ md5sum: 9dcdc9577c0fdbb25089eda210267546 - name: stringtie merge forward-strand stub - command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config -stub-run tags: - stringtie - stringtie/merge @@ -58,7 +58,7 @@ - path: output/stringtie/test.transcripts.gtf - name: stringtie merge test_stringtie_reverse_merge stub - command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/merge/nextflow.config -stub-run tags: - stringtie - stringtie/merge diff --git a/tests/modules/nf-core/stringtie/stringtie/test.yml b/tests/modules/nf-core/stringtie/stringtie/test.yml index 034b88d3808..8d0ba91ea1f 100644 --- a/tests/modules/nf-core/stringtie/stringtie/test.yml +++ b/tests/modules/nf-core/stringtie/stringtie/test.yml @@ -1,5 +1,5 @@ - name: stringtie stringtie forward - command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config + command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config tags: - stringtie - stringtie/stringtie @@ -20,7 +20,7 @@ md5sum: e981c0038295ae54b63cedb1083f1540 - name: stringtie stringtie reverse - command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config + command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config tags: - stringtie - stringtie/stringtie @@ -41,7 +41,7 @@ md5sum: e981c0038295ae54b63cedb1083f1540 - name: stringtie stringtie forward stub - command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config -stub-run tags: - stringtie - stringtie/stringtie @@ -52,7 +52,7 @@ - path: ./output/stringtie/test.ballgown - name: stringtie stringtie reverse stub - command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/stringtie/stringtie/nextflow.config -stub-run tags: - stringtie - stringtie/stringtie diff --git a/tests/modules/nf-core/subread/featurecounts/test.yml b/tests/modules/nf-core/subread/featurecounts/test.yml index 7cc24457b96..b6ec04f4c22 100644 --- a/tests/modules/nf-core/subread/featurecounts/test.yml +++ b/tests/modules/nf-core/subread/featurecounts/test.yml @@ -1,5 +1,5 @@ - name: subread featurecounts test_subread_featurecounts_forward - command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_forward -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config + command: nextflow run ./tests/modules/nf-core/subread/featurecounts -entry test_subread_featurecounts_forward -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/subread/featurecounts/nextflow.config tags: - subread - subread/featurecounts @@ -10,7 +10,7 @@ md5sum: 8f602ff9a8ef467af43294e80b367cdf - name: subread featurecounts test_subread_featurecounts_reverse - command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config + command: nextflow run ./tests/modules/nf-core/subread/featurecounts -entry test_subread_featurecounts_reverse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/subread/featurecounts/nextflow.config tags: - subread - subread/featurecounts @@ -21,7 +21,7 @@ md5sum: 7cfa30ad678b9bc1bc63afbb0281547b - name: subread featurecounts test_subread_featurecounts_unstranded - command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config + command: nextflow run ./tests/modules/nf-core/subread/featurecounts -entry test_subread_featurecounts_unstranded -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/subread/featurecounts/nextflow.config tags: - subread - subread/featurecounts diff --git a/tests/modules/nf-core/svdb/merge/test.yml b/tests/modules/nf-core/svdb/merge/test.yml index 5af282aeeaa..88e61469e4c 100644 --- a/tests/modules/nf-core/svdb/merge/test.yml +++ b/tests/modules/nf-core/svdb/merge/test.yml @@ -1,19 +1,19 @@ - name: svdb merge test_svdb_merge - command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/merge/nextflow.config tags: - svdb - svdb/merge files: - path: output/svdb/test_sv_merge.vcf.gz - name: svdb merge test_svdb_merge_noprio - command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config + command: nextflow run ./tests/modules/nf-core/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/merge/nextflow.config tags: - svdb - svdb/merge files: - path: output/svdb/test_sv_merge.vcf.gz - name: svdb merge test_svdb_merge_noprio stub - command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config -stub + command: nextflow run ./tests/modules/nf-core/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/merge/nextflow.config -stub tags: - svdb - svdb/merge diff --git a/tests/modules/nf-core/svdb/query/test.yml b/tests/modules/nf-core/svdb/query/test.yml index a7cbe3a681c..7f683efe6bf 100644 --- a/tests/modules/nf-core/svdb/query/test.yml +++ b/tests/modules/nf-core/svdb/query/test.yml @@ -1,5 +1,5 @@ - name: svdb query - command: nextflow run ./tests/modules/svdb/query -entry test_svdb_query -c ./tests/config/nextflow.config -c ./tests/modules/svdb/query/nextflow.config + command: nextflow run ./tests/modules/nf-core/svdb/query -entry test_svdb_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/query/nextflow.config tags: - svdb - svdb/query @@ -7,7 +7,7 @@ - path: output/svdb/test_query.vcf - name: svdb query multiple - command: nextflow run ./tests/modules/svdb/query -entry test_svdb_query_multiple -c ./tests/config/nextflow.config -c ./tests/modules/svdb/query/nextflow.config + command: nextflow run ./tests/modules/nf-core/svdb/query -entry test_svdb_query_multiple -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svdb/query/nextflow.config tags: - svdb - svdb/query diff --git a/tests/modules/nf-core/svtk/standardize/test.yml b/tests/modules/nf-core/svtk/standardize/test.yml index 764cfe2fc67..cd0e9ea2ab7 100644 --- a/tests/modules/nf-core/svtk/standardize/test.yml +++ b/tests/modules/nf-core/svtk/standardize/test.yml @@ -1,5 +1,5 @@ - name: svtk standardize test_svtk_standardize - command: nextflow run ./tests/modules/svtk/standardize -entry test_svtk_standardize -c ./tests/config/nextflow.config -c ./tests/modules/svtk/standardize/nextflow.config + command: nextflow run ./tests/modules/nf-core/svtk/standardize -entry test_svtk_standardize -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/standardize/nextflow.config tags: - svtk - svtk/standardize @@ -17,7 +17,7 @@ md5sum: f7530f3bc7e6020e758cc996adc8ae35 - name: svtk standardize test_svtk_standardize_no_contigs - command: nextflow run ./tests/modules/svtk/standardize -entry test_svtk_standardize_no_contigs -c ./tests/config/nextflow.config -c ./tests/modules/svtk/standardize/nextflow.config + command: nextflow run ./tests/modules/nf-core/svtk/standardize -entry test_svtk_standardize_no_contigs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/svtk/standardize/nextflow.config tags: - svtk - svtk/standardize diff --git a/tests/modules/nf-core/tabix/bgzip/test.yml b/tests/modules/nf-core/tabix/bgzip/test.yml index 53e00ccbf6e..906e509ecb2 100644 --- a/tests/modules/nf-core/tabix/bgzip/test.yml +++ b/tests/modules/nf-core/tabix/bgzip/test.yml @@ -1,5 +1,5 @@ - name: tabix bgzip compress - command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_compress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/bgzip -entry test_tabix_bgzip_compress -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgzip/nextflow.config tags: - tabix - tabix/bgzip @@ -9,7 +9,7 @@ - path: ./output/tabix/test.vcf.gz.gzi should_exist: false - name: tabix bgzip compress gzi - command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_compress_gzi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/bgzip -entry test_tabix_bgzip_compress_gzi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgzip/nextflow.config tags: - tabix - tabix/bgzip @@ -19,7 +19,7 @@ - path: ./output/tabix/test.vcf.gz.gzi md5sum: 7dea362b3fac8e00956a4952a3d4f474 - name: tabix bgzip decompress - command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip_decompress -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/bgzip -entry test_tabix_bgzip_decompress -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgzip/nextflow.config tags: - tabix - tabix/bgzip diff --git a/tests/modules/nf-core/tabix/bgziptabix/test.yml b/tests/modules/nf-core/tabix/bgziptabix/test.yml index ed614d7efa4..78ce288b321 100644 --- a/tests/modules/nf-core/tabix/bgziptabix/test.yml +++ b/tests/modules/nf-core/tabix/bgziptabix/test.yml @@ -1,5 +1,5 @@ - name: tabix bgziptabix test_tabix_bgziptabix - command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgziptabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/bgziptabix/nextflow.config tags: - tabix/bgziptabix - tabix diff --git a/tests/modules/nf-core/tabix/tabix/test.yml b/tests/modules/nf-core/tabix/tabix/test.yml index 6d168ef5d9c..9457790b178 100644 --- a/tests/modules/nf-core/tabix/tabix/test.yml +++ b/tests/modules/nf-core/tabix/tabix/test.yml @@ -1,5 +1,5 @@ - name: tabix tabix bed - command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix @@ -7,7 +7,7 @@ - path: ./output/tabix/test.bed.gz.tbi md5sum: 5b40851ab6b8ccf7946313c86481c0df - name: tabix tabix gff - command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix @@ -15,7 +15,7 @@ - path: ./output/tabix/genome.gff3.gz.tbi md5sum: f79a67d95a98076e04fbe0455d825926 - name: tabix tabix vcf - command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix @@ -23,7 +23,7 @@ - path: output/tabix/test.vcf.gz.tbi md5sum: 36e11bf96ed0af4a92caa91a68612d64 - name: tabix tabix vcf csi - command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix diff --git a/tests/modules/nf-core/tailfindr/test.yml b/tests/modules/nf-core/tailfindr/test.yml index 16f08c4e1a9..ac4f13d492d 100644 --- a/tests/modules/nf-core/tailfindr/test.yml +++ b/tests/modules/nf-core/tailfindr/test.yml @@ -1,5 +1,5 @@ - name: "tailfindr" - command: nextflow run ./tests/modules/tailfindr -entry test_tailfindr -c ./tests/config/nextflow.config -c ./tests/modules/tailfindr/nextflow.config + command: nextflow run ./tests/modules/nf-core/tailfindr -entry test_tailfindr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tailfindr/nextflow.config tags: - "tailfindr" files: diff --git a/tests/modules/nf-core/tbprofiler/profile/test.yml b/tests/modules/nf-core/tbprofiler/profile/test.yml index 6e30b784499..24eaa37e511 100644 --- a/tests/modules/nf-core/tbprofiler/profile/test.yml +++ b/tests/modules/nf-core/tbprofiler/profile/test.yml @@ -1,5 +1,5 @@ - name: tbprofiler profile illumina - command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config + command: nextflow run ./tests/modules/nf-core/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tbprofiler/profile/nextflow.config tags: - tbprofiler - tbprofiler/profile @@ -10,7 +10,7 @@ - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz - name: tbprofiler profile nanopore - command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config + command: nextflow run ./tests/modules/nf-core/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tbprofiler/profile/nextflow.config tags: - tbprofiler - tbprofiler/profile diff --git a/tests/modules/nf-core/tiddit/cov/test.yml b/tests/modules/nf-core/tiddit/cov/test.yml index 916cc9e38b7..5bbdbda16f4 100644 --- a/tests/modules/nf-core/tiddit/cov/test.yml +++ b/tests/modules/nf-core/tiddit/cov/test.yml @@ -1,5 +1,5 @@ - name: tiddit cov test_tiddit_cov_cram_bed - command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config tags: - tiddit - tiddit/cov @@ -8,7 +8,7 @@ md5sum: 3b1a28c62a5f25bbba77c1042e9abdf7 - name: tiddit cov test_tiddit_cov_bam_bed - command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config tags: - tiddit - tiddit/cov @@ -17,7 +17,7 @@ md5sum: 9d1474f1c7c6516205254077087bb026 - name: tiddit cov test_tiddit_cov_cram_wig - command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config tags: - tiddit - tiddit/cov @@ -26,7 +26,7 @@ md5sum: ca3645fd0c3491c86c075c91d16d57c4 - name: tiddit cov test_tiddit_cov_bam_wig - command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/cov/nextflow.config tags: - tiddit - tiddit/cov diff --git a/tests/modules/nf-core/tiddit/sv/test.yml b/tests/modules/nf-core/tiddit/sv/test.yml index 5bbfe4aea93..e8a0974065e 100644 --- a/tests/modules/nf-core/tiddit/sv/test.yml +++ b/tests/modules/nf-core/tiddit/sv/test.yml @@ -1,5 +1,5 @@ - name: tiddit sv test_tiddit_sv_bam - command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config tags: - tiddit - tiddit/sv @@ -10,7 +10,7 @@ md5sum: 157907671297c34bacfd3e73eff9bbdf - name: tiddit sv test_tiddit_sv_cram - command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config tags: - tiddit - tiddit/sv @@ -21,7 +21,7 @@ md5sum: 56687eeffa452f78f18d54a69dd17c78 - name: tiddit sv test_tiddit_sv_nobwa_bam - command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_nobwa_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config tags: - tiddit - tiddit/sv @@ -32,7 +32,7 @@ md5sum: ddac94f9cd4f991b6ce2052d7f78a525 - name: tiddit sv test_tiddit_sv_nobwa_cram - command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config + command: nextflow run ./tests/modules/nf-core/tiddit/sv -entry test_tiddit_sv_nobwa_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiddit/sv/nextflow.config tags: - tiddit - tiddit/sv diff --git a/tests/modules/nf-core/transdecoder/longorf/test.yml b/tests/modules/nf-core/transdecoder/longorf/test.yml index 4e88f0e824e..f45de1b502d 100644 --- a/tests/modules/nf-core/transdecoder/longorf/test.yml +++ b/tests/modules/nf-core/transdecoder/longorf/test.yml @@ -1,5 +1,5 @@ - name: transdecoder longorf test_transdecoder_longorf - command: nextflow run tests/modules/transdecoder/longorf -entry test_transdecoder_longorf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/transdecoder/longorf -entry test_transdecoder_longorf -c tests/config/nextflow.config tags: - transdecoder - transdecoder/longorf diff --git a/tests/modules/nf-core/transdecoder/predict/test.yml b/tests/modules/nf-core/transdecoder/predict/test.yml index cf2c0d0770b..88575684df3 100644 --- a/tests/modules/nf-core/transdecoder/predict/test.yml +++ b/tests/modules/nf-core/transdecoder/predict/test.yml @@ -1,5 +1,5 @@ - name: transdecoder predict test_transdecoder_predict - command: nextflow run tests/modules/transdecoder/predict -entry test_transdecoder_predict -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/transdecoder/predict -entry test_transdecoder_predict -c tests/config/nextflow.config tags: - transdecoder - transdecoder/predict diff --git a/tests/modules/nf-core/trimgalore/test.yml b/tests/modules/nf-core/trimgalore/test.yml index ecbd2b5af38..5351d273c10 100644 --- a/tests/modules/nf-core/trimgalore/test.yml +++ b/tests/modules/nf-core/trimgalore/test.yml @@ -1,5 +1,5 @@ - name: trimgalore single-end - command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimgalore/nextflow.config + command: nextflow run ./tests/modules/nf-core/trimgalore/ -entry test_trimgalore_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimgalore/nextflow.config tags: - trimgalore files: @@ -9,7 +9,7 @@ - path: ./output/trimgalore/test_trimmed.fq.gz - name: trimgalore paired-end - command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimgalore/nextflow.config + command: nextflow run ./tests/modules/nf-core/trimgalore/ -entry test_trimgalore_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimgalore/nextflow.config tags: - trimgalore files: diff --git a/tests/modules/nf-core/trimmomatic/test.yml b/tests/modules/nf-core/trimmomatic/test.yml index 12fe44fa385..b2813597d9b 100644 --- a/tests/modules/nf-core/trimmomatic/test.yml +++ b/tests/modules/nf-core/trimmomatic/test.yml @@ -1,5 +1,5 @@ - name: trimmomatic single-end - command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config + command: nextflow run ./tests/modules/nf-core/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimmomatic/nextflow.config tags: - "trimmomatic" files: @@ -8,7 +8,7 @@ md5sum: e4c3f619e9b0e26847f8f3e3d9af319b - name: trimmomatic paired-end - command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config + command: nextflow run ./tests/modules/nf-core/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimmomatic/nextflow.config tags: - "trimmomatic" files: @@ -20,7 +20,7 @@ - path: "output/trimmomatic/test.unpaired.trim_2.fastq.gz" - name: trimmomatic no adapter specified - command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config + command: nextflow run ./tests/modules/nf-core/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/trimmomatic/nextflow.config tags: - "trimmomatic" exit_code: 1 diff --git a/tests/modules/nf-core/ucsc/bedclip/test.yml b/tests/modules/nf-core/ucsc/bedclip/test.yml index bcf22c71d0c..55da06df78b 100755 --- a/tests/modules/nf-core/ucsc/bedclip/test.yml +++ b/tests/modules/nf-core/ucsc/bedclip/test.yml @@ -1,5 +1,5 @@ - name: ucsc bedclip - command: nextflow run ./tests/modules/ucsc/bedclip -entry test_ucsc_bedclip -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedclip/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/bedclip -entry test_ucsc_bedclip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedclip/nextflow.config tags: - ucsc - ucsc/bedclip diff --git a/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml b/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml index 2a532a62ab0..34b28baa2fa 100644 --- a/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml +++ b/tests/modules/nf-core/ucsc/bedgraphtobigwig/test.yml @@ -1,5 +1,5 @@ - name: ucsc bedgraphtobigwig - command: nextflow run ./tests/modules/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedgraphtobigwig/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedgraphtobigwig/nextflow.config tags: - ucsc - ucsc/bedgraphtobigwig diff --git a/tests/modules/nf-core/ucsc/bedtobigbed/test.yml b/tests/modules/nf-core/ucsc/bedtobigbed/test.yml index 718b1864bab..e17777359b7 100644 --- a/tests/modules/nf-core/ucsc/bedtobigbed/test.yml +++ b/tests/modules/nf-core/ucsc/bedtobigbed/test.yml @@ -1,5 +1,5 @@ - name: ucsc bedtobigbed - command: nextflow run ./tests/modules/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedtobigbed/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedtobigbed/nextflow.config tags: - ucsc - ucsc/bedtobigbed @@ -7,7 +7,7 @@ - path: output/ucsc/test.bigBed md5sum: 3c2400aab8f7a3ac333905c7484d9a24 - name: ucsc bedtobigbed autosql - command: nextflow run ./tests/modules/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed_autosql -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedtobigbed/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/bedtobigbed -entry test_ucsc_bedtobigbed_autosql -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bedtobigbed/nextflow.config tags: - ucsc - ucsc/bedtobigbed diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml index 7344c9440cc..07661349ef2 100644 --- a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml +++ b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/test.yml @@ -1,5 +1,5 @@ - name: ucsc bigwigaverageoverbed test_ucsc_bigwigaverageoverbed - command: nextflow run ./tests/modules/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bigwigaverageoverbed/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/bigwigaverageoverbed/nextflow.config tags: - ucsc - ucsc/bigwigaverageoverbed diff --git a/tests/modules/nf-core/ucsc/liftover/test.yml b/tests/modules/nf-core/ucsc/liftover/test.yml index c301618986a..16f20b5e2b8 100644 --- a/tests/modules/nf-core/ucsc/liftover/test.yml +++ b/tests/modules/nf-core/ucsc/liftover/test.yml @@ -1,5 +1,5 @@ - name: ucsc liftover test_ucsc_liftover - command: nextflow run ./tests/modules/ucsc/liftover -entry test_ucsc_liftover -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/liftover/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/liftover -entry test_ucsc_liftover -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/liftover/nextflow.config tags: - ucsc - ucsc/liftover diff --git a/tests/modules/nf-core/ucsc/wigtobigwig/test.yml b/tests/modules/nf-core/ucsc/wigtobigwig/test.yml index aa478bc319c..79decdbc64a 100644 --- a/tests/modules/nf-core/ucsc/wigtobigwig/test.yml +++ b/tests/modules/nf-core/ucsc/wigtobigwig/test.yml @@ -1,5 +1,5 @@ - name: ucsc wigtobigwig test_ucsc_wigtobigwig - command: nextflow run ./tests/modules/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/wigtobigwig/nextflow.config + command: nextflow run ./tests/modules/nf-core/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/wigtobigwig/nextflow.config tags: - ucsc - ucsc/wigtobigwig @@ -10,7 +10,7 @@ md5sum: 7e14421c65faf5165389f34806acdb12 - name: ucsc wigtobigwig test_ucsc_wigtobigwig stub - command: nextflow run ./tests/modules/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/wigtobigwig/nextflow.config -stub + command: nextflow run ./tests/modules/nf-core/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/wigtobigwig/nextflow.config -stub tags: - ucsc - ucsc/wigtobigwig diff --git a/tests/modules/nf-core/ultra/align/test.yml b/tests/modules/nf-core/ultra/align/test.yml index 7e26f9a5fb5..1eafd64295e 100644 --- a/tests/modules/nf-core/ultra/align/test.yml +++ b/tests/modules/nf-core/ultra/align/test.yml @@ -1,5 +1,5 @@ - name: ultra align test_ultra_align - command: nextflow run ./tests/modules/ultra/align -entry test_ultra_align -c ./tests/config/nextflow.config -c ./tests/modules/ultra/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/ultra/align -entry test_ultra_align -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ultra/align/nextflow.config tags: - ultra/align - ultra diff --git a/tests/modules/nf-core/ultra/index/test.yml b/tests/modules/nf-core/ultra/index/test.yml index 36dcf093b92..2e192ea684b 100644 --- a/tests/modules/nf-core/ultra/index/test.yml +++ b/tests/modules/nf-core/ultra/index/test.yml @@ -1,5 +1,5 @@ - name: ultra index test_ultra_index - command: nextflow run ./tests/modules/ultra/index -entry test_ultra_index -c ./tests/config/nextflow.config -c ./tests/modules/ultra/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/ultra/index -entry test_ultra_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ultra/index/nextflow.config tags: - ultra - ultra/index diff --git a/tests/modules/nf-core/ultra/pipeline/test.yml b/tests/modules/nf-core/ultra/pipeline/test.yml index d424ba73613..4abfbcf2182 100644 --- a/tests/modules/nf-core/ultra/pipeline/test.yml +++ b/tests/modules/nf-core/ultra/pipeline/test.yml @@ -1,5 +1,5 @@ - name: ultra pipeline test_ultra_pipeline - command: nextflow run ./tests/modules/ultra/pipeline -entry test_ultra_pipeline -c ./tests/config/nextflow.config -c ./tests/modules/ultra/pipeline/nextflow.config + command: nextflow run ./tests/modules/nf-core/ultra/pipeline -entry test_ultra_pipeline -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ultra/pipeline/nextflow.config tags: - ultra - ultra/pipeline diff --git a/tests/modules/nf-core/umitools/dedup/test.yml b/tests/modules/nf-core/umitools/dedup/test.yml index 5a92a35a29d..157c67cabb4 100644 --- a/tests/modules/nf-core/umitools/dedup/test.yml +++ b/tests/modules/nf-core/umitools/dedup/test.yml @@ -1,5 +1,5 @@ - name: umitools dedup test_umitools_dedup_no_umi - command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config tags: - umitools/dedup - umitools @@ -7,7 +7,7 @@ - path: output/umitools/test.dedup.bam - name: umitools dedup test_umitools_dedup_single_end_no_stats - command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config tags: - umitools/dedup - umitools @@ -31,7 +31,7 @@ - path: output/umitools/test.umi_extract.log - name: umitools dedup test_umitools_dedup_paired_end_no_stats - command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config tags: - umitools/dedup - umitools @@ -56,7 +56,7 @@ - path: output/umitools/test.umi_extract_2.fastq.gz - name: umitools dedup test_umitools_dedup_paired_end_stats - command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/umitools/dedup/nextflow.config tags: - umitools/dedup - umitools diff --git a/tests/modules/nf-core/umitools/extract/test.yml b/tests/modules/nf-core/umitools/extract/test.yml index 336cd1229f8..7f2b8a0a9b7 100644 --- a/tests/modules/nf-core/umitools/extract/test.yml +++ b/tests/modules/nf-core/umitools/extract/test.yml @@ -1,5 +1,5 @@ - name: umitools extract test_umitools_extract_single_end - command: nextflow run tests/modules/umitools/extract -entry test_umitools_extract_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_single_end -c tests/config/nextflow.config tags: - umitools/extract - umitools @@ -12,7 +12,7 @@ md5sum: 397e6972343f9d7b8eae387fc18c12c7 - name: umitools extract test_umitools_extract_paired_end - command: nextflow run tests/modules/umitools/extract -entry test_umitools_extract_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_paired_end -c tests/config/nextflow.config tags: - umitools/extract - umitools diff --git a/tests/modules/nf-core/unicycler/test.yml b/tests/modules/nf-core/unicycler/test.yml index e25845aab50..61bb0d9c692 100644 --- a/tests/modules/nf-core/unicycler/test.yml +++ b/tests/modules/nf-core/unicycler/test.yml @@ -1,5 +1,5 @@ - name: unicycler test_unicycler_single_end - command: nextflow run ./tests/modules/unicycler -entry test_unicycler_single_end -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config + command: nextflow run ./tests/modules/nf-core/unicycler -entry test_unicycler_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unicycler/nextflow.config tags: - unicycler files: @@ -10,7 +10,7 @@ - "Assembly complete" - name: unicycler test_unicycler_paired_end - command: nextflow run ./tests/modules/unicycler -entry test_unicycler_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config + command: nextflow run ./tests/modules/nf-core/unicycler -entry test_unicycler_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unicycler/nextflow.config tags: - unicycler files: @@ -21,7 +21,7 @@ - "Assembly complete" - name: unicycler test_unicycler_shortreads_longreads - command: nextflow run ./tests/modules/unicycler -entry test_unicycler_shortreads_longreads -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config + command: nextflow run ./tests/modules/nf-core/unicycler -entry test_unicycler_shortreads_longreads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unicycler/nextflow.config tags: - unicycler files: diff --git a/tests/modules/nf-core/untar/test.yml b/tests/modules/nf-core/untar/test.yml index 8ebb2d12768..a314e167b12 100644 --- a/tests/modules/nf-core/untar/test.yml +++ b/tests/modules/nf-core/untar/test.yml @@ -1,5 +1,5 @@ - name: untar test_untar - command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config + command: nextflow run ./tests/modules/nf-core/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/untar/nextflow.config tags: - untar files: @@ -11,7 +11,7 @@ md5sum: 094d5891cdccf2f1468088855c214b2c - name: untar test_untar_different_output_path - command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config + command: nextflow run ./tests/modules/nf-core/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/untar/nextflow.config tags: - untar files: @@ -19,7 +19,7 @@ md5sum: 03038959f4dd181c86bc97ae71fe270a - name: untar test_untar_onlyfiles - command: nextflow run ./tests/modules/untar -entry test_untar_onlyfiles -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config + command: nextflow run ./tests/modules/nf-core/untar -entry test_untar_onlyfiles -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/untar/nextflow.config tags: - untar files: diff --git a/tests/modules/nf-core/unzip/test.yml b/tests/modules/nf-core/unzip/test.yml index 8016b4fa5ba..0e02cbe07ee 100644 --- a/tests/modules/nf-core/unzip/test.yml +++ b/tests/modules/nf-core/unzip/test.yml @@ -1,5 +1,5 @@ - name: unzip - command: nextflow run ./tests/modules/unzip -entry test_unzip -c ./tests/config/nextflow.config -c ./tests/modules/unzip/nextflow.config + command: nextflow run ./tests/modules/nf-core/unzip -entry test_unzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unzip/nextflow.config tags: - unzip files: diff --git a/tests/modules/nf-core/vardictjava/test.yml b/tests/modules/nf-core/vardictjava/test.yml index d7ff54c0dd2..1f516da1d9e 100644 --- a/tests/modules/nf-core/vardictjava/test.yml +++ b/tests/modules/nf-core/vardictjava/test.yml @@ -1,5 +1,5 @@ - name: vardictjava test_vardictjava_bam - command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava_bam -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config + command: nextflow run ./tests/modules/nf-core/vardictjava -entry test_vardictjava_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vardictjava/nextflow.config tags: - vardictjava files: diff --git a/tests/modules/nf-core/variantbam/test.yml b/tests/modules/nf-core/variantbam/test.yml index 1c9550ed8d3..60ec26a6b97 100644 --- a/tests/modules/nf-core/variantbam/test.yml +++ b/tests/modules/nf-core/variantbam/test.yml @@ -1,5 +1,5 @@ - name: variantbam test_variantbam - command: nextflow run ./tests/modules/variantbam -entry test_variantbam -c ./tests/config/nextflow.config -c ./tests/modules/variantbam/nextflow.config + command: nextflow run ./tests/modules/nf-core/variantbam -entry test_variantbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/variantbam/nextflow.config tags: - variantbam files: diff --git a/tests/modules/nf-core/vcf2db/test.yml b/tests/modules/nf-core/vcf2db/test.yml index df276b1c72d..5b37f4218d8 100644 --- a/tests/modules/nf-core/vcf2db/test.yml +++ b/tests/modules/nf-core/vcf2db/test.yml @@ -1,5 +1,5 @@ - name: vcf2db test_vcf2db - command: nextflow run ./tests/modules/vcf2db -entry test_vcf2db -c ./tests/config/nextflow.config -c ./tests/modules/vcf2db/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcf2db -entry test_vcf2db -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2db/nextflow.config tags: - vcf2db files: diff --git a/tests/modules/nf-core/vcf2maf/test.yml b/tests/modules/nf-core/vcf2maf/test.yml index c0a7b4eb0d1..e62e39f8e43 100644 --- a/tests/modules/nf-core/vcf2maf/test.yml +++ b/tests/modules/nf-core/vcf2maf/test.yml @@ -1,5 +1,5 @@ - name: vcf2maf test_vcf2maf_no_vep - command: nextflow run ./tests/modules/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config -c ./tests/modules/vcf2maf/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2maf/nextflow.config tags: - vcf2maf files: @@ -7,7 +7,7 @@ md5sum: c7f357efa774fd5c4003d84f05212ed0 - name: vcf2maf test_vcf2maf_vep - command: nextflow run ./tests/modules/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config -c ./tests/modules/vcf2maf/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2maf/nextflow.config tags: - vcf2maf files: diff --git a/tests/modules/nf-core/vcfanno/test.yml b/tests/modules/nf-core/vcfanno/test.yml index cb9a8b044b4..fe1d8cf9a05 100644 --- a/tests/modules/nf-core/vcfanno/test.yml +++ b/tests/modules/nf-core/vcfanno/test.yml @@ -1,5 +1,5 @@ - name: vcfanno test_vcfanno - command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno -c ./tests/config/nextflow.config -c ./tests/modules/vcfanno/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcfanno -entry test_vcfanno -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcfanno/nextflow.config tags: - vcfanno files: @@ -11,7 +11,7 @@ md5sum: 90ceb2fd2e06e781846d69c3981db665 - name: vcfanno test_vcfanno_uncompressed - command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno_uncompressed -c ./tests/config/nextflow.config -c ./tests/modules/vcfanno/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcfanno -entry test_vcfanno_uncompressed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcfanno/nextflow.config tags: - vcfanno files: diff --git a/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml b/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml index d8ed82db392..b730c5a12b0 100644 --- a/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml +++ b/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml @@ -1,5 +1,5 @@ - name: vcflib vcfbreakmulti - command: nextflow run ./tests/modules/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config tags: - vcflib/vcfbreakmulti - vcflib @@ -8,7 +8,7 @@ md5sum: 666d2d970399cf219dc1dc1eadff9170 - name: vcflib vcfbreakmulti stub - command: nextflow run ./tests/modules/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config -stub + command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config -stub tags: - vcflib/vcfbreakmulti - vcflib diff --git a/tests/modules/nf-core/vcflib/vcfuniq/test.yml b/tests/modules/nf-core/vcflib/vcfuniq/test.yml index aadcd77facc..f51c7b0c7f3 100644 --- a/tests/modules/nf-core/vcflib/vcfuniq/test.yml +++ b/tests/modules/nf-core/vcflib/vcfuniq/test.yml @@ -1,5 +1,5 @@ - name: vcflib vcfuniq - command: nextflow run ./tests/modules/vcflib/vcfuniq -entry test_vcflib_vcfuniq -c ./tests/config/nextflow.config -c ./tests/modules/vcflib/vcfuniq/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcflib/vcfuniq -entry test_vcflib_vcfuniq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcflib/vcfuniq/nextflow.config tags: - vcflib - vcflib/vcfuniq diff --git a/tests/modules/nf-core/vcftools/test.yml b/tests/modules/nf-core/vcftools/test.yml index 5314ea75804..e0a1e31f1a2 100644 --- a/tests/modules/nf-core/vcftools/test.yml +++ b/tests/modules/nf-core/vcftools/test.yml @@ -1,5 +1,5 @@ - name: vcftools test_vcftools_vcf_base - command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcf_base -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcf_base -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config tags: - vcftools files: @@ -7,7 +7,7 @@ md5sum: 7f126655f17268fd1a338734f62868e9 - name: vcftools test_vcftools_vcfgz_base - command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcfgz_base -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcfgz_base -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config tags: - vcftools files: @@ -15,7 +15,7 @@ md5sum: 7f126655f17268fd1a338734f62868e9 - name: vcftools test_vcftools_vcf_optional - command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcf_optional -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcf_optional -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config tags: - vcftools files: @@ -23,7 +23,7 @@ md5sum: 7f126655f17268fd1a338734f62868e9 - name: vcftools test_vcftools_vcfgz_optional - command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcfgz_optional -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcftools -entry test_vcftools_vcfgz_optional -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcftools/nextflow.config tags: - vcftools files: diff --git a/tests/modules/nf-core/vsearch/sintax/test.yml b/tests/modules/nf-core/vsearch/sintax/test.yml index 5c5abd0a6c6..70f6d1bbaa3 100644 --- a/tests/modules/nf-core/vsearch/sintax/test.yml +++ b/tests/modules/nf-core/vsearch/sintax/test.yml @@ -1,5 +1,5 @@ - name: vsearch sintax test_vsearch_sintax - command: nextflow run ./tests/modules/vsearch/sintax -entry test_vsearch_sintax -c ./tests/config/nextflow.config -c ./tests/modules/vsearch/sintax/nextflow.config + command: nextflow run ./tests/modules/nf-core/vsearch/sintax -entry test_vsearch_sintax -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vsearch/sintax/nextflow.config tags: - vsearch - vsearch/sintax diff --git a/tests/modules/nf-core/vsearch/usearchglobal/test.yml b/tests/modules/nf-core/vsearch/usearchglobal/test.yml index 227d728f047..9dcc8db45df 100644 --- a/tests/modules/nf-core/vsearch/usearchglobal/test.yml +++ b/tests/modules/nf-core/vsearch/usearchglobal/test.yml @@ -1,5 +1,5 @@ - name: vsearch usearchglobal test_vsearch_usearchglobal - command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal -c ./tests/config/nextflow.config -c ./tests/modules/vsearch/usearchglobal/nextflow.config + command: nextflow run ./tests/modules/nf-core/vsearch/usearchglobal -entry test_vsearch_usearchglobal -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vsearch/usearchglobal/nextflow.config tags: - vsearch/usearchglobal - vsearch @@ -17,7 +17,7 @@ - "21291 cols, 21290 ids (100.0%), 1 gaps (0.0%)" - name: vsearch usearchglobal test_vsearch_usearchglobal_userout - command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal_userout -c ./tests/config/nextflow.config -c ./tests/modules/vsearch/usearchglobal/nextflow.config + command: nextflow run ./tests/modules/nf-core/vsearch/usearchglobal -entry test_vsearch_usearchglobal_userout -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vsearch/usearchglobal/nextflow.config tags: - vsearch/usearchglobal - vsearch diff --git a/tests/modules/nf-core/whamg/test.yml b/tests/modules/nf-core/whamg/test.yml index 33f1a9507c7..2e1323a22b9 100644 --- a/tests/modules/nf-core/whamg/test.yml +++ b/tests/modules/nf-core/whamg/test.yml @@ -1,5 +1,5 @@ - name: whamg test_whamg_bam - command: nextflow run ./tests/modules/whamg -entry test_whamg_bam -c ./tests/config/nextflow.config -c ./tests/modules/whamg/nextflow.config + command: nextflow run ./tests/modules/nf-core/whamg -entry test_whamg_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/whamg/nextflow.config tags: - whamg files: diff --git a/tests/modules/nf-core/yara/index/test.yml b/tests/modules/nf-core/yara/index/test.yml index a8d178661f9..973e08d441a 100644 --- a/tests/modules/nf-core/yara/index/test.yml +++ b/tests/modules/nf-core/yara/index/test.yml @@ -1,5 +1,5 @@ - name: yara index test_yara_index - command: nextflow run ./tests/modules/yara/index -entry test_yara_index -c ./tests/config/nextflow.config -c ./tests/modules/yara/index/nextflow.config + command: nextflow run ./tests/modules/nf-core/yara/index -entry test_yara_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/yara/index/nextflow.config tags: - yara/index - yara diff --git a/tests/modules/nf-core/yara/mapper/test.yml b/tests/modules/nf-core/yara/mapper/test.yml index 3bfddc5b5c3..93e4f39b709 100644 --- a/tests/modules/nf-core/yara/mapper/test.yml +++ b/tests/modules/nf-core/yara/mapper/test.yml @@ -1,5 +1,5 @@ - name: yara mapper test_yara_single_end - command: nextflow run ./tests/modules/yara/mapper -entry test_yara_single_end -c ./tests/config/nextflow.config -c ./tests/modules/yara/mapper/nextflow.config + command: nextflow run ./tests/modules/nf-core/yara/mapper -entry test_yara_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/yara/mapper/nextflow.config tags: - yara/mapper - yara @@ -34,7 +34,7 @@ md5sum: 6e9fe4042a72f2345f644f239272b7e6 - name: yara mapper test_yara_paired_end - command: nextflow run ./tests/modules/yara/mapper -entry test_yara_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/yara/mapper/nextflow.config + command: nextflow run ./tests/modules/nf-core/yara/mapper -entry test_yara_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/yara/mapper/nextflow.config tags: - yara/mapper - yara From 4c25cb810b0aacd24aec044dac7dd9f89416dc35 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 19:08:54 +0100 Subject: [PATCH 7/9] Standardise path to tests/config to ./tests/config everywhere --- tests/modules/nf-core/abricate/run/test.yml | 2 +- .../modules/nf-core/abricate/summary/test.yml | 2 +- tests/modules/nf-core/adapterremoval/test.yml | 6 +++--- .../nf-core/adapterremovalfixprefix/test.yml | 2 +- tests/modules/nf-core/amplify/predict/test.yml | 2 +- .../nf-core/amrfinderplus/update/test.yml | 2 +- .../nf-core/antismash/antismashlite/test.yml | 2 +- .../antismashlitedownloaddatabases/test.yml | 2 +- tests/modules/nf-core/ascat/test.yml | 2 +- .../modules/nf-core/atlas/splitmerge/test.yml | 2 +- tests/modules/nf-core/bakta/test.yml | 2 +- tests/modules/nf-core/bamcmp/test.yml | 2 +- .../modules/nf-core/bamtools/convert/test.yml | 18 +++++++++--------- .../modules/nf-core/bcftools/annotate/test.yml | 4 ++-- tests/modules/nf-core/bcftools/sort/test.yml | 2 +- .../biobambam/bammarkduplicates2/test.yml | 2 +- tests/modules/nf-core/biscuit/align/test.yml | 4 ++-- .../nf-core/biscuit/biscuitblaster/test.yml | 4 ++-- tests/modules/nf-core/biscuit/bsconv/test.yml | 2 +- tests/modules/nf-core/biscuit/epiread/test.yml | 6 +++--- tests/modules/nf-core/biscuit/index/test.yml | 2 +- tests/modules/nf-core/biscuit/mergecg/test.yml | 2 +- tests/modules/nf-core/biscuit/pileup/test.yml | 4 ++-- tests/modules/nf-core/biscuit/qc/test.yml | 2 +- tests/modules/nf-core/biscuit/vcf2bed/test.yml | 2 +- tests/modules/nf-core/bowtie2/align/test.yml | 6 +++--- tests/modules/nf-core/bracken/bracken/test.yml | 8 ++++---- .../nf-core/cellranger/mkfastq/test.yml | 4 ++-- .../nf-core/centrifuge/centrifuge/test.yml | 4 ++-- .../modules/nf-core/cnvpytor/callcnvs/test.yml | 4 ++-- .../nf-core/cnvpytor/histogram/test.yml | 4 ++-- .../nf-core/cnvpytor/importreaddepth/test.yml | 8 ++++---- .../nf-core/cnvpytor/partition/test.yml | 4 ++-- tests/modules/nf-core/cnvpytor/view/test.yml | 6 +++--- .../controlfreec/assesssignificance/test.yml | 4 ++-- .../nf-core/controlfreec/freec/test.yml | 4 ++-- .../nf-core/controlfreec/freec2bed/test.yml | 4 ++-- .../nf-core/controlfreec/freec2circos/test.yml | 4 ++-- .../nf-core/controlfreec/makegraph/test.yml | 4 ++-- tests/modules/nf-core/dastool/dastool/test.yml | 2 +- .../nf-core/dastool/fastatocontig2bin/test.yml | 4 ++-- .../nf-core/dastool/scaffolds2bin/test.yml | 4 ++-- .../nf-core/deeparg/downloaddata/test.yml | 2 +- tests/modules/nf-core/deeparg/predict/test.yml | 2 +- tests/modules/nf-core/deepvariant/test.yml | 4 ++-- tests/modules/nf-core/diamond/blastp/test.yml | 4 ++-- tests/modules/nf-core/diamond/makedb/test.yml | 2 +- tests/modules/nf-core/elprep/filter/test.yml | 2 +- tests/modules/nf-core/elprep/merge/test.yml | 2 +- tests/modules/nf-core/elprep/split/test.yml | 2 +- tests/modules/nf-core/faqcs/test.yml | 4 ++-- tests/modules/nf-core/freebayes/test.yml | 10 +++++----- tests/modules/nf-core/gamma/gamma/test.yml | 4 ++-- tests/modules/nf-core/gatk4/applybqsr/test.yml | 6 +++--- .../nf-core/gatk4/applybqsrspark/test.yml | 6 +++--- tests/modules/nf-core/gatk4/applyvqsr/test.yml | 4 ++-- .../gatk4/calculatecontamination/test.yml | 6 +++--- .../nf-core/gatk4/combinegvcfs/test.yml | 2 +- .../modules/nf-core/gatk4/fastqtosam/test.yml | 4 ++-- .../nf-core/gatk4/gatherbqsrreports/test.yml | 4 ++-- .../nf-core/gatk4/genomicsdbimport/test.yml | 6 +++--- .../nf-core/gatk4/getpileupsummaries/test.yml | 4 ++-- .../nf-core/gatk4/indexfeaturefile/test.yml | 8 ++++---- .../gatk4/markduplicatesspark/nextflow.config | 2 +- .../nf-core/gatk4/selectvariants/test.yml | 4 ++-- .../nf-core/gatk4/splitintervals/test.yml | 4 ++-- .../nf-core/gatk4/splitncigarreads/test.yml | 4 ++-- .../nf-core/gatk4/variantrecalibrator/test.yml | 4 ++-- tests/modules/nf-core/genomescope2/test.yml | 2 +- .../nf-core/gstama/polyacleanup/test.yml | 2 +- .../nf-core/hamronization/deeparg/test.yml | 2 +- tests/modules/nf-core/happy/happy/test.yml | 4 ++-- tests/modules/nf-core/happy/prepy/test.yml | 4 ++-- .../nf-core/hmmcopy/generatemap/test.yml | 2 +- .../nf-core/hmmcopy/mapcounter/test.yml | 2 +- .../nf-core/hmmcopy/readcounter/test.yml | 2 +- tests/modules/nf-core/hmmer/eslalimask/main.nf | 2 +- .../modules/nf-core/hmmer/eslreformat/main.nf | 6 +++--- tests/modules/nf-core/hmmer/hmmalign/main.nf | 4 ++-- tests/modules/nf-core/hmmer/hmmsearch/test.yml | 4 ++-- tests/modules/nf-core/hpsuissero/test.yml | 2 +- .../nf-core/ichorcna/createpon/test.yml | 4 ++-- tests/modules/nf-core/ichorcna/run/test.yml | 4 ++-- tests/modules/nf-core/kaiju/kaiju/test.yml | 4 ++-- .../modules/nf-core/kaiju/kaiju2table/test.yml | 2 +- tests/modules/nf-core/kat/hist/test.yml | 4 ++-- tests/modules/nf-core/kraken2/kraken2/test.yml | 6 +++--- .../nf-core/krona/ktimporttext/test.yml | 4 ++-- tests/modules/nf-core/legsta/test.yml | 2 +- tests/modules/nf-core/mafft/test.yml | 2 +- tests/modules/nf-core/mash/dist/test.yml | 2 +- tests/modules/nf-core/maxquant/lfq/test.yml | 2 +- tests/modules/nf-core/md5sum/test.yml | 2 +- tests/modules/nf-core/megan/rma2info/test.yml | 2 +- tests/modules/nf-core/meryl/count/test.yml | 4 ++-- tests/modules/nf-core/meryl/histogram/test.yml | 2 +- tests/modules/nf-core/meryl/unionsum/test.yml | 4 ++-- .../modules/nf-core/metabat2/metabat2/test.yml | 4 ++-- tests/modules/nf-core/minimap2/align/test.yml | 4 ++-- tests/modules/nf-core/mobsuite/recon/test.yml | 2 +- .../modules/nf-core/motus/downloaddb/test.yml | 2 +- tests/modules/nf-core/motus/profile/test.yml | 2 +- .../nf-core/msisensorpro/msi_somatic/test.yml | 2 +- .../modules/nf-core/msisensorpro/scan/test.yml | 2 +- .../modules/nf-core/ngscheckmate/ncm/test.yml | 4 ++-- tests/modules/nf-core/panaroo/run/test.yml | 2 +- .../nf-core/phantompeakqualtools/test.yml | 4 ++-- .../picard/addorreplacereadgroups/test.yml | 4 ++-- tests/modules/nf-core/picard/cleansam/test.yml | 2 +- .../picard/createsequencedictionary/test.yml | 2 +- .../nf-core/picard/fixmateinformation/test.yml | 2 +- .../nf-core/picard/liftovervcf/test.yml | 4 ++-- tests/modules/nf-core/plink2/extract/test.yml | 2 +- tests/modules/nf-core/plink2/score/test.yml | 2 +- tests/modules/nf-core/plink2/vcf/test.yml | 2 +- tests/modules/nf-core/prinseqplusplus/test.yml | 4 ++-- .../nf-core/qualimap/bamqccram/test.yml | 2 +- .../modules/nf-core/rtgtools/vcfeval/test.yml | 4 ++-- tests/modules/nf-core/samtools/bam2fq/test.yml | 4 ++-- .../modules/nf-core/samtools/convert/test.yml | 4 ++-- tests/modules/nf-core/samtools/dict/test.yml | 2 +- tests/modules/nf-core/samtools/faidx/test.yml | 4 ++-- .../modules/nf-core/samtools/mpileup/test.yml | 4 ++-- tests/modules/nf-core/seqkit/pair/test.yml | 2 +- tests/modules/nf-core/seqkit/replace/test.yml | 4 ++-- tests/modules/nf-core/seqkit/split2/test.yml | 12 ++++++------ tests/modules/nf-core/seqkit/stats/test.yml | 10 +++++----- tests/modules/nf-core/seqtk/rename/test.yml | 4 ++-- tests/modules/nf-core/seqtk/seq/test.yml | 4 ++-- tests/modules/nf-core/sexdeterrmine/test.yml | 2 +- tests/modules/nf-core/shasum/test.yml | 2 +- tests/modules/nf-core/shigatyper/test.yml | 6 +++--- tests/modules/nf-core/sistr/test.yml | 2 +- tests/modules/nf-core/slimfastq/test.yml | 8 ++++---- .../modules/nf-core/snapaligner/index/test.yml | 2 +- tests/modules/nf-core/snippy/run/test.yml | 2 +- tests/modules/nf-core/snpsift/split/test.yml | 6 +++--- tests/modules/nf-core/sourmash/sketch/test.yml | 2 +- tests/modules/nf-core/srst2/srst2/main.nf | 4 ++-- tests/modules/nf-core/srst2/srst2/test.yml | 8 ++++---- tests/modules/nf-core/ssuissero/test.yml | 2 +- .../nf-core/stadeniolib/scramble/test.yml | 2 +- tests/modules/nf-core/stranger/test.yml | 6 +++--- .../nf-core/transdecoder/longorf/test.yml | 2 +- .../nf-core/transdecoder/predict/test.yml | 2 +- .../modules/nf-core/umitools/extract/test.yml | 4 ++-- .../nf-core/vcflib/vcfbreakmulti/test.yml | 4 ++-- 147 files changed, 266 insertions(+), 266 deletions(-) diff --git a/tests/modules/nf-core/abricate/run/test.yml b/tests/modules/nf-core/abricate/run/test.yml index 809dd888d74..76d8d751ea9 100644 --- a/tests/modules/nf-core/abricate/run/test.yml +++ b/tests/modules/nf-core/abricate/run/test.yml @@ -1,5 +1,5 @@ - name: abricate run - command: nextflow run ./tests/modules/nf-core/abricate/run -entry test_abricate_run -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/abricate/run -entry test_abricate_run -c ./tests/config/nextflow.config tags: - abricate - abricate/run diff --git a/tests/modules/nf-core/abricate/summary/test.yml b/tests/modules/nf-core/abricate/summary/test.yml index 6c110b8ce6f..17ef0a7f34e 100644 --- a/tests/modules/nf-core/abricate/summary/test.yml +++ b/tests/modules/nf-core/abricate/summary/test.yml @@ -1,5 +1,5 @@ - name: abricate summary - command: nextflow run ./tests/modules/nf-core/abricate/summary -entry test_abricate_summary -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/abricate/summary -entry test_abricate_summary -c ./tests/config/nextflow.config tags: - abricate - abricate/summary diff --git a/tests/modules/nf-core/adapterremoval/test.yml b/tests/modules/nf-core/adapterremoval/test.yml index 63aafa5f77a..a17312019ef 100644 --- a/tests/modules/nf-core/adapterremoval/test.yml +++ b/tests/modules/nf-core/adapterremoval/test.yml @@ -1,5 +1,5 @@ - name: adapterremoval test_adapterremoval_single_end - command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config tags: - adapterremoval files: @@ -12,7 +12,7 @@ md5sum: ac5b46719719b7ee62739530b80869fc - name: adapterremoval test_adapterremoval_paired_end - command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config tags: - adapterremoval files: @@ -27,7 +27,7 @@ md5sum: fa621c887897da5a379c719399c17db7 - name: adapterremoval test_adapterremoval_paired_end_collapse - command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config tags: - adapterremoval files: diff --git a/tests/modules/nf-core/adapterremovalfixprefix/test.yml b/tests/modules/nf-core/adapterremovalfixprefix/test.yml index 8e7de8c72b2..f1ae13832d6 100644 --- a/tests/modules/nf-core/adapterremovalfixprefix/test.yml +++ b/tests/modules/nf-core/adapterremovalfixprefix/test.yml @@ -1,5 +1,5 @@ - name: adapterremovalfixprefix test_adapterremovalfixprefix - command: nextflow run ./tests/modules/nf-core/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c ./tests/config/nextflow.config tags: - adapterremovalfixprefix files: diff --git a/tests/modules/nf-core/amplify/predict/test.yml b/tests/modules/nf-core/amplify/predict/test.yml index 285475def61..ce5c8531a82 100644 --- a/tests/modules/nf-core/amplify/predict/test.yml +++ b/tests/modules/nf-core/amplify/predict/test.yml @@ -1,5 +1,5 @@ - name: amplify predict amplify_predict - command: nextflow run ./tests/modules/nf-core/amplify/predict -entry amplify_predict -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/amplify/predict -entry amplify_predict -c ./tests/config/nextflow.config tags: - amplify/predict - amplify diff --git a/tests/modules/nf-core/amrfinderplus/update/test.yml b/tests/modules/nf-core/amrfinderplus/update/test.yml index b201dab695e..83c699bc3d4 100644 --- a/tests/modules/nf-core/amrfinderplus/update/test.yml +++ b/tests/modules/nf-core/amrfinderplus/update/test.yml @@ -1,5 +1,5 @@ - name: amrfinderplus update test_amrfinderplus_update - command: nextflow run ./tests/modules/nf-core/amrfinderplus/update -entry test_amrfinderplus_update -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/amrfinderplus/update -entry test_amrfinderplus_update -c ./tests/config/nextflow.config tags: - amrfinderplus - amrfinderplus/update diff --git a/tests/modules/nf-core/antismash/antismashlite/test.yml b/tests/modules/nf-core/antismash/antismashlite/test.yml index e64ba816f1e..63119336a49 100644 --- a/tests/modules/nf-core/antismash/antismashlite/test.yml +++ b/tests/modules/nf-core/antismash/antismashlite/test.yml @@ -1,5 +1,5 @@ - name: antismash antismashlite test_antismashlite - command: nextflow run ./tests/modules/nf-core/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/antismash/antismashlite -entry test_antismashlite -c ./tests/config/nextflow.config tags: - antismash/antismashlite - antismash diff --git a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml index c21f8128144..98739d6cc19 100644 --- a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml @@ -1,5 +1,5 @@ - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases - command: nextflow run ./tests/modules/nf-core/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c ./tests/config/nextflow.config tags: - antismash/antismashlitedownloaddatabases - antismash diff --git a/tests/modules/nf-core/ascat/test.yml b/tests/modules/nf-core/ascat/test.yml index 2b97d948985..760f4b0e8b4 100644 --- a/tests/modules/nf-core/ascat/test.yml +++ b/tests/modules/nf-core/ascat/test.yml @@ -1,5 +1,5 @@ - name: ascat test_ascat - command: nextflow run ./tests/modules/nf-core/ascat -entry test_ascat -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/ascat -entry test_ascat -c ./tests/config/nextflow.config -stub-run tags: - ascat files: diff --git a/tests/modules/nf-core/atlas/splitmerge/test.yml b/tests/modules/nf-core/atlas/splitmerge/test.yml index e891f10dfed..c41c8e06a69 100644 --- a/tests/modules/nf-core/atlas/splitmerge/test.yml +++ b/tests/modules/nf-core/atlas/splitmerge/test.yml @@ -1,5 +1,5 @@ - name: atlas splitmerge test_atlas_splitmerge - command: nextflow run ./tests/modules/nf-core/atlas/splitmerge -entry test_atlas_splitmerge -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/atlas/splitmerge -entry test_atlas_splitmerge -c ./tests/config/nextflow.config tags: - atlas - atlas/splitmerge diff --git a/tests/modules/nf-core/bakta/test.yml b/tests/modules/nf-core/bakta/test.yml index 428a27d37ac..1b046eec01b 100644 --- a/tests/modules/nf-core/bakta/test.yml +++ b/tests/modules/nf-core/bakta/test.yml @@ -1,5 +1,5 @@ - name: bakta - command: nextflow run ./tests/modules/nf-core/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/bakta -entry test_bakta -c ./tests/config/nextflow.config -stub-run tags: - bakta files: diff --git a/tests/modules/nf-core/bamcmp/test.yml b/tests/modules/nf-core/bamcmp/test.yml index 5d59fc3a892..a7b65bae1f5 100644 --- a/tests/modules/nf-core/bamcmp/test.yml +++ b/tests/modules/nf-core/bamcmp/test.yml @@ -1,5 +1,5 @@ - name: bamcmp test_bamcmp - command: nextflow run ./tests/modules/nf-core/bamcmp -entry test_bamcmp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamcmp -entry test_bamcmp -c ./tests/config/nextflow.config tags: - bamcmp files: diff --git a/tests/modules/nf-core/bamtools/convert/test.yml b/tests/modules/nf-core/bamtools/convert/test.yml index 16c70e03f1d..f930f0d5846 100644 --- a/tests/modules/nf-core/bamtools/convert/test.yml +++ b/tests/modules/nf-core/bamtools/convert/test.yml @@ -1,19 +1,19 @@ - name: bamtools convert test_bamtools_convert_ext_error - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_ext_error -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert exit_code: 1 - name: bamtools convert test_bamtools_convert_noext_error - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_noext_error -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert exit_code: 1 - name: bamtools convert test_bamtools_convert_bed - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_bed -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -24,7 +24,7 @@ md5sum: eb7a144b8a97965d3482f6f96b8a8243 - name: bamtools convert test_bamtools_convert_fasta - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fasta -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -35,7 +35,7 @@ md5sum: 42d19a2b2b07f05edb82b34369dfd754 - name: bamtools convert test_bamtools_convert_fastq - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_fastq -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -46,7 +46,7 @@ md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e - name: bamtools convert test_bamtools_convert_json - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_json -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -57,7 +57,7 @@ md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3 - name: bamtools convert test_bamtools_convert_pileup - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_pileup -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -68,7 +68,7 @@ md5sum: fd3ad0edd1e085b1a002e0593d1d5814 - name: bamtools convert test_bamtools_convert_sam - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_sam -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert @@ -79,7 +79,7 @@ md5sum: 4be470ce3cc0143ae5ae415b612a4965 - name: bamtools convert test_bamtools_convert_yaml - command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bamtools/convert -entry test_bamtools_convert_yaml -c ./tests/config/nextflow.config tags: - bamtools - bamtools/convert diff --git a/tests/modules/nf-core/bcftools/annotate/test.yml b/tests/modules/nf-core/bcftools/annotate/test.yml index 34084b50fb0..22027d3e5de 100644 --- a/tests/modules/nf-core/bcftools/annotate/test.yml +++ b/tests/modules/nf-core/bcftools/annotate/test.yml @@ -1,5 +1,5 @@ - name: bcftools annotate test_bcftools_annotate_out_vcf - command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c ./tests/config/nextflow.config tags: - bcftools/annotate - bcftools @@ -9,7 +9,7 @@ md5sum: ff237d88fce62300fdab66b284e9aa95 - name: bcftools annotate test_bcftools_annotate_out_bcf - command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c ./tests/config/nextflow.config tags: - bcftools/annotate - bcftools diff --git a/tests/modules/nf-core/bcftools/sort/test.yml b/tests/modules/nf-core/bcftools/sort/test.yml index f1e12c54b7d..c51da8b2441 100644 --- a/tests/modules/nf-core/bcftools/sort/test.yml +++ b/tests/modules/nf-core/bcftools/sort/test.yml @@ -1,5 +1,5 @@ - name: bcftools sort test_bcftools_sort - command: nextflow run ./tests/modules/nf-core/bcftools/sort -entry test_bcftools_sort -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/sort -entry test_bcftools_sort -c ./tests/config/nextflow.config tags: - bcftools - bcftools/sort diff --git a/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml b/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml index 3e280b383ab..2d838f1fc6e 100644 --- a/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml +++ b/tests/modules/nf-core/biobambam/bammarkduplicates2/test.yml @@ -1,5 +1,5 @@ - name: biobambam bammarkduplicates2 test_biobambam_bammarkduplicates2 - command: nextflow run ./tests/modules/nf-core/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c ./tests/config/nextflow.config tags: - biobambam/bammarkduplicates2 - biobambam diff --git a/tests/modules/nf-core/biscuit/align/test.yml b/tests/modules/nf-core/biscuit/align/test.yml index fff02b26a24..95ff9411ce9 100644 --- a/tests/modules/nf-core/biscuit/align/test.yml +++ b/tests/modules/nf-core/biscuit/align/test.yml @@ -1,5 +1,5 @@ - name: biscuit align test_biscuit_align_single - command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_single -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_single -c ./tests/config/nextflow.config tags: - biscuit - biscuit/align @@ -26,7 +26,7 @@ md5sum: a86c4170bbf90cc75b93eb59ea124acd - name: biscuit align test_biscuit_align_paired - command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_paired -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/align -entry test_biscuit_align_paired -c ./tests/config/nextflow.config tags: - biscuit - biscuit/align diff --git a/tests/modules/nf-core/biscuit/biscuitblaster/test.yml b/tests/modules/nf-core/biscuit/biscuitblaster/test.yml index 03b44837bf6..c1f9abb55db 100644 --- a/tests/modules/nf-core/biscuit/biscuitblaster/test.yml +++ b/tests/modules/nf-core/biscuit/biscuitblaster/test.yml @@ -1,5 +1,5 @@ - name: biscuit biscuitblaster test_biscuit_blaster_single - command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c ./tests/config/nextflow.config tags: - biscuit/biscuitblaster - biscuit @@ -28,7 +28,7 @@ md5sum: bfb660b5b0d92dde6817a1c6a2a302bb - name: biscuit biscuitblaster test_biscuit_blaster_paired - command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c ./tests/config/nextflow.config tags: - biscuit/biscuitblaster - biscuit diff --git a/tests/modules/nf-core/biscuit/bsconv/test.yml b/tests/modules/nf-core/biscuit/bsconv/test.yml index 737f3d1ae80..db50a552354 100644 --- a/tests/modules/nf-core/biscuit/bsconv/test.yml +++ b/tests/modules/nf-core/biscuit/bsconv/test.yml @@ -1,5 +1,5 @@ - name: biscuit bsconv test_biscuit_bsconv - command: nextflow run ./tests/modules/nf-core/biscuit/bsconv -entry test_biscuit_bsconv -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/bsconv -entry test_biscuit_bsconv -c ./tests/config/nextflow.config tags: - biscuit - biscuit/bsconv diff --git a/tests/modules/nf-core/biscuit/epiread/test.yml b/tests/modules/nf-core/biscuit/epiread/test.yml index 7cd1fe9d210..23ab6aa3b71 100644 --- a/tests/modules/nf-core/biscuit/epiread/test.yml +++ b/tests/modules/nf-core/biscuit/epiread/test.yml @@ -1,5 +1,5 @@ - name: biscuit epiread test_biscuit_epiread_nosnp - command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_nosnp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_nosnp -c ./tests/config/nextflow.config tags: - biscuit - biscuit/epiread @@ -26,7 +26,7 @@ md5sum: 674a77ac5ca8f4b42d30e58e30c3a9af - name: biscuit epiread test_biscuit_epiread_snp - command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp -c ./tests/config/nextflow.config tags: - biscuit - biscuit/epiread @@ -53,7 +53,7 @@ md5sum: f2f7c4ff3c6a135b1c8a3aff24a44d81 - name: biscuit epiread test_biscuit_epiread_snp_decompress - command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c ./tests/config/nextflow.config tags: - biscuit - biscuit/epiread diff --git a/tests/modules/nf-core/biscuit/index/test.yml b/tests/modules/nf-core/biscuit/index/test.yml index 73fdde94d6f..c14a3f00103 100644 --- a/tests/modules/nf-core/biscuit/index/test.yml +++ b/tests/modules/nf-core/biscuit/index/test.yml @@ -1,5 +1,5 @@ - name: biscuit index test_biscuit_index - command: nextflow run ./tests/modules/nf-core/biscuit/index -entry test_biscuit_index -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/index -entry test_biscuit_index -c ./tests/config/nextflow.config tags: - biscuit/index - biscuit diff --git a/tests/modules/nf-core/biscuit/mergecg/test.yml b/tests/modules/nf-core/biscuit/mergecg/test.yml index 2aca1b25176..7b16d1646cd 100644 --- a/tests/modules/nf-core/biscuit/mergecg/test.yml +++ b/tests/modules/nf-core/biscuit/mergecg/test.yml @@ -1,5 +1,5 @@ - name: biscuit mergecg test_biscuit_mergecg - command: nextflow run ./tests/modules/nf-core/biscuit/mergecg -entry test_biscuit_mergecg -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/mergecg -entry test_biscuit_mergecg -c ./tests/config/nextflow.config tags: - biscuit - biscuit/mergecg diff --git a/tests/modules/nf-core/biscuit/pileup/test.yml b/tests/modules/nf-core/biscuit/pileup/test.yml index dd02371dd7c..318a662dee1 100644 --- a/tests/modules/nf-core/biscuit/pileup/test.yml +++ b/tests/modules/nf-core/biscuit/pileup/test.yml @@ -1,5 +1,5 @@ - name: biscuit pileup test_biscuit_pileup - command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup -c ./tests/config/nextflow.config tags: - biscuit - biscuit/pileup @@ -26,7 +26,7 @@ md5sum: ae38b891fdbf9f7ff5c486408f949dc5 - name: biscuit pileup test_biscuit_pileup_somatic - command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup_somatic -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/pileup -entry test_biscuit_pileup_somatic -c ./tests/config/nextflow.config tags: - biscuit - biscuit/pileup diff --git a/tests/modules/nf-core/biscuit/qc/test.yml b/tests/modules/nf-core/biscuit/qc/test.yml index 4655e39c3c0..2cd8ca7c432 100644 --- a/tests/modules/nf-core/biscuit/qc/test.yml +++ b/tests/modules/nf-core/biscuit/qc/test.yml @@ -1,5 +1,5 @@ - name: biscuit qc test_biscuit_qc - command: nextflow run ./tests/modules/nf-core/biscuit/qc -entry test_biscuit_qc -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/qc -entry test_biscuit_qc -c ./tests/config/nextflow.config tags: - biscuit/qc - biscuit diff --git a/tests/modules/nf-core/biscuit/vcf2bed/test.yml b/tests/modules/nf-core/biscuit/vcf2bed/test.yml index ee00d493171..ad4f9a1aa76 100644 --- a/tests/modules/nf-core/biscuit/vcf2bed/test.yml +++ b/tests/modules/nf-core/biscuit/vcf2bed/test.yml @@ -1,5 +1,5 @@ - name: biscuit vcf2bed test_biscuit_vcf2bed - command: nextflow run ./tests/modules/nf-core/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c ./tests/config/nextflow.config tags: - biscuit/vcf2bed - biscuit diff --git a/tests/modules/nf-core/bowtie2/align/test.yml b/tests/modules/nf-core/bowtie2/align/test.yml index f9944d60897..5ec73575c51 100644 --- a/tests/modules/nf-core/bowtie2/align/test.yml +++ b/tests/modules/nf-core/bowtie2/align/test.yml @@ -19,7 +19,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_paired_end - command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config tags: - bowtie2 - bowtie2/align @@ -29,7 +29,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_single_end_large_index - command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index tags: - bowtie2 - bowtie2/align @@ -39,7 +39,7 @@ - path: ./output/bowtie2/versions.yml - name: bowtie2 align test_bowtie2_align_paired_end_large_index - command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index + command: nextflow run ./tests/modules/nf-core/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bowtie2/align/nextflow.config --force_large_index tags: - bowtie2 - bowtie2/align diff --git a/tests/modules/nf-core/bracken/bracken/test.yml b/tests/modules/nf-core/bracken/bracken/test.yml index cb64523d770..c35a12a7a48 100644 --- a/tests/modules/nf-core/bracken/bracken/test.yml +++ b/tests/modules/nf-core/bracken/bracken/test.yml @@ -1,5 +1,5 @@ - name: bracken bracken test_bracken_bracken_single_end_default_args - command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c ./tests/config/nextflow.config tags: - bracken/bracken - bracken @@ -10,7 +10,7 @@ md5sum: e0abdac999c0d58becd8c868dd12028b - name: bracken bracken test_bracken_bracken_single_end_custom_args - command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c ./tests/config/nextflow.config tags: - bracken/bracken - bracken @@ -21,7 +21,7 @@ md5sum: 7d0a1629ece197a8062271d39ed8ef74 - name: bracken bracken test_bracken_bracken_paired_end_default_args - command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c ./tests/config/nextflow.config tags: - bracken/bracken - bracken @@ -32,7 +32,7 @@ md5sum: 7b58898d0b9cce1ca170ac5a82d8ecf1 - name: bracken bracken test_bracken_bracken_paired_end_custom_args - command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c ./tests/config/nextflow.config tags: - bracken/bracken - bracken diff --git a/tests/modules/nf-core/cellranger/mkfastq/test.yml b/tests/modules/nf-core/cellranger/mkfastq/test.yml index dec205d6938..2279c842729 100644 --- a/tests/modules/nf-core/cellranger/mkfastq/test.yml +++ b/tests/modules/nf-core/cellranger/mkfastq/test.yml @@ -1,12 +1,12 @@ - name: cellranger mkfastq test_cellranger_mkfastq_simple - command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run tags: - cellranger - cellranger/mkfastq files: - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz - name: cellranger mkfastq test_cellranger_mkfastq_illumina - command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkfastq/nextflow.config -stub-run tags: - cellranger - cellranger/mkfastq diff --git a/tests/modules/nf-core/centrifuge/centrifuge/test.yml b/tests/modules/nf-core/centrifuge/centrifuge/test.yml index 322e087865a..6d1a64a5e33 100644 --- a/tests/modules/nf-core/centrifuge/centrifuge/test.yml +++ b/tests/modules/nf-core/centrifuge/centrifuge/test.yml @@ -1,5 +1,5 @@ - name: centrifuge centrifuge test_centrifuge_centrifuge_single_end - command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c ./tests/config/nextflow.config tags: - centrifuge - centrifuge/centrifuge @@ -10,7 +10,7 @@ - path: output/centrifuge/versions.yml - name: centrifuge centrifuge test_centrifuge_centrifuge_paired_end - command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c ./tests/config/nextflow.config tags: - centrifuge - centrifuge/centrifuge diff --git a/tests/modules/nf-core/cnvpytor/callcnvs/test.yml b/tests/modules/nf-core/cnvpytor/callcnvs/test.yml index 3ee825a01db..7d3f8fe1ffd 100644 --- a/tests/modules/nf-core/cnvpytor/callcnvs/test.yml +++ b/tests/modules/nf-core/cnvpytor/callcnvs/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor callcnvs test_cnvpytor_callcnvs - command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/callcnvs @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor callcnvs test_cnvpytor_callcnvs stub - command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c ./tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/callcnvs diff --git a/tests/modules/nf-core/cnvpytor/histogram/test.yml b/tests/modules/nf-core/cnvpytor/histogram/test.yml index aa10ac14f4a..a25fc3902af 100644 --- a/tests/modules/nf-core/cnvpytor/histogram/test.yml +++ b/tests/modules/nf-core/cnvpytor/histogram/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor histogram test_cnvpytor_histogram - command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/histogram @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor histogram test_cnvpytor_histogram stub - command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/histogram -entry test_cnvpytor_histogram -c ./tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/histogram diff --git a/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml b/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml index ea1fed954c2..9e62d1c1df0 100644 --- a/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml +++ b/tests/modules/nf-core/cnvpytor/importreaddepth/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth - command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/importreaddepth @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub - command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c ./tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/importreaddepth @@ -17,7 +17,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram - command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/importreaddepth @@ -26,7 +26,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub - command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c ./tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/importreaddepth diff --git a/tests/modules/nf-core/cnvpytor/partition/test.yml b/tests/modules/nf-core/cnvpytor/partition/test.yml index 28a9651f96e..88eff3b6bd4 100644 --- a/tests/modules/nf-core/cnvpytor/partition/test.yml +++ b/tests/modules/nf-core/cnvpytor/partition/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor partition test_cnvpytor_partition - command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/partition @@ -8,7 +8,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor partition test_cnvpytor_partition stub - command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/partition -entry test_cnvpytor_partition -c ./tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/partition diff --git a/tests/modules/nf-core/cnvpytor/view/test.yml b/tests/modules/nf-core/cnvpytor/view/test.yml index 42307d52d38..f8b54e2d7c1 100644 --- a/tests/modules/nf-core/cnvpytor/view/test.yml +++ b/tests/modules/nf-core/cnvpytor/view/test.yml @@ -1,5 +1,5 @@ - name: cnvpytor view test_cnvpytor_view - command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/view @@ -9,7 +9,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor view test_cnvpytor_view tsv - command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_tsvout -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_tsvout -c ./tests/config/nextflow.config tags: - cnvpytor - cnvpytor/view @@ -18,7 +18,7 @@ - path: output/cnvpytor/versions.yml - name: cnvpytor view test_cnvpytor_view stub - command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_stub -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/cnvpytor/view -entry test_cnvpytor_view_stub -c ./tests/config/nextflow.config -stub-run tags: - cnvpytor - cnvpytor/view diff --git a/tests/modules/nf-core/controlfreec/assesssignificance/test.yml b/tests/modules/nf-core/controlfreec/assesssignificance/test.yml index 4928e028d80..94740f8fa0a 100644 --- a/tests/modules/nf-core/controlfreec/assesssignificance/test.yml +++ b/tests/modules/nf-core/controlfreec/assesssignificance/test.yml @@ -1,5 +1,5 @@ - name: controlfreec assesssignificance test_controlfreec_assesssignificance - command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c ./tests/config/nextflow.config tags: - controlfreec/assesssignificance - controlfreec @@ -9,7 +9,7 @@ - path: output/controlfreec/versions.yml - name: controlfreec assesssignificance test_controlfreec_assesssignificance_single - command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c ./tests/config/nextflow.config -stub-run tags: - controlfreec/assesssignificance - controlfreec diff --git a/tests/modules/nf-core/controlfreec/freec/test.yml b/tests/modules/nf-core/controlfreec/freec/test.yml index df9fda5a4c8..c0096876bc9 100644 --- a/tests/modules/nf-core/controlfreec/freec/test.yml +++ b/tests/modules/nf-core/controlfreec/freec/test.yml @@ -1,5 +1,5 @@ - name: controlfreec test_controlfreec_freec - command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec -c ./tests/config/nextflow.config tags: - controlfreec - controlfreec/freec @@ -22,7 +22,7 @@ - path: output/controlfreec/versions.yml - name: controlfreec test_controlfreec_freec_single - command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/freec -entry test_controlfreec_freec_single -c ./tests/config/nextflow.config -stub-run tags: - controlfreec - controlfreec/freec diff --git a/tests/modules/nf-core/controlfreec/freec2bed/test.yml b/tests/modules/nf-core/controlfreec/freec2bed/test.yml index 4a97fbfc68e..9a632817e00 100644 --- a/tests/modules/nf-core/controlfreec/freec2bed/test.yml +++ b/tests/modules/nf-core/controlfreec/freec2bed/test.yml @@ -1,5 +1,5 @@ - name: controlfreec freec2bed test_controlfreec_freec2bed - command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c ./tests/config/nextflow.config tags: - controlfreec/freec2bed - controlfreec @@ -8,7 +8,7 @@ md5sum: abe10b7ce94ba903503e697394c17297 - name: controlfreec freec2bed test_controlfreec_freec2bed_single - command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c ./tests/config/nextflow.config -stub-run tags: - controlfreec/freec2bed - controlfreec diff --git a/tests/modules/nf-core/controlfreec/freec2circos/test.yml b/tests/modules/nf-core/controlfreec/freec2circos/test.yml index 2d0a807dd5b..6fa51b7ec1c 100644 --- a/tests/modules/nf-core/controlfreec/freec2circos/test.yml +++ b/tests/modules/nf-core/controlfreec/freec2circos/test.yml @@ -1,5 +1,5 @@ - name: controlfreec freec2circos test_controlfreec_freec2circos - command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c ./tests/config/nextflow.config tags: - controlfreec - controlfreec/freec2circos @@ -8,7 +8,7 @@ md5sum: 19cf35f2c36b46f717dc8342b8a5a645 - name: controlfreec freec2circos test_controlfreec_freec2circos_single - command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c ./tests/config/nextflow.config -stub-run tags: - controlfreec - controlfreec/freec2circos diff --git a/tests/modules/nf-core/controlfreec/makegraph/test.yml b/tests/modules/nf-core/controlfreec/makegraph/test.yml index b51a1ca9c1b..803b0889336 100644 --- a/tests/modules/nf-core/controlfreec/makegraph/test.yml +++ b/tests/modules/nf-core/controlfreec/makegraph/test.yml @@ -1,5 +1,5 @@ - name: controlfreec makegraph test_controlfreec_makegraph - command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph -c ./tests/config/nextflow.config tags: - controlfreec - controlfreec/makegraph @@ -12,7 +12,7 @@ md5sum: 1435b29536b3b1555b4c423f8f4fb000 - name: controlfreec makegraph test_controlfreec_makegraph_single - command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c ./tests/config/nextflow.config -stub-run tags: - controlfreec - controlfreec/makegraph diff --git a/tests/modules/nf-core/dastool/dastool/test.yml b/tests/modules/nf-core/dastool/dastool/test.yml index d802cbba8e1..de6609ca158 100644 --- a/tests/modules/nf-core/dastool/dastool/test.yml +++ b/tests/modules/nf-core/dastool/dastool/test.yml @@ -1,5 +1,5 @@ - name: dastool dastool test_dastool_dastool - command: nextflow run ./tests/modules/nf-core/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/dastool -entry test_dastool_dastool -c ./tests/config/nextflow.config tags: - dastool/dastool - dastool diff --git a/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml b/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml index 6c6dd8a652f..4333a72594a 100644 --- a/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml +++ b/tests/modules/nf-core/dastool/fastatocontig2bin/test.yml @@ -1,5 +1,5 @@ - name: dastool fastatocontig2bin test_dastool_fastatocontig2bin - command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c ./tests/config/nextflow.config tags: - dastool - dastool/fastatocontig2bin @@ -10,7 +10,7 @@ md5sum: ff4b6f14bee4548bf09b5e602c306595 - name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped - command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c ./tests/config/nextflow.config tags: - dastool - dastool/fastatocontig2bin diff --git a/tests/modules/nf-core/dastool/scaffolds2bin/test.yml b/tests/modules/nf-core/dastool/scaffolds2bin/test.yml index 40e73615e47..2dcf828f1ae 100644 --- a/tests/modules/nf-core/dastool/scaffolds2bin/test.yml +++ b/tests/modules/nf-core/dastool/scaffolds2bin/test.yml @@ -1,5 +1,5 @@ - name: dastool scaffolds2bin test_dastool_scaffolds2bin - command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c ./tests/config/nextflow.config tags: - dastool - dastool/scaffolds2bin @@ -9,7 +9,7 @@ - path: output/dastool/versions.yml md5sum: d0831ed159eb5a1a1565d1d211012ad6 - name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped - command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c ./tests/config/nextflow.config tags: - dastool - dastool/scaffolds2bin diff --git a/tests/modules/nf-core/deeparg/downloaddata/test.yml b/tests/modules/nf-core/deeparg/downloaddata/test.yml index 1a4b08f6351..bae89614206 100644 --- a/tests/modules/nf-core/deeparg/downloaddata/test.yml +++ b/tests/modules/nf-core/deeparg/downloaddata/test.yml @@ -1,5 +1,5 @@ - name: deeparg downloaddata test_deeparg_downloaddata - command: nextflow run ./tests/modules/nf-core/deeparg/downloaddata -entry test_deeparg_downloaddata -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeparg/downloaddata -entry test_deeparg_downloaddata -c ./tests/config/nextflow.config tags: - deeparg - deeparg/downloaddata diff --git a/tests/modules/nf-core/deeparg/predict/test.yml b/tests/modules/nf-core/deeparg/predict/test.yml index 20977ce28c4..fc8398aa20a 100644 --- a/tests/modules/nf-core/deeparg/predict/test.yml +++ b/tests/modules/nf-core/deeparg/predict/test.yml @@ -1,5 +1,5 @@ - name: deeparg predict test_deeparg_predict - command: nextflow run ./tests/modules/nf-core/deeparg/predict -entry test_deeparg_predict -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deeparg/predict -entry test_deeparg_predict -c ./tests/config/nextflow.config tags: - deeparg/predict - deeparg diff --git a/tests/modules/nf-core/deepvariant/test.yml b/tests/modules/nf-core/deepvariant/test.yml index 88f377fd566..e5901cb743f 100644 --- a/tests/modules/nf-core/deepvariant/test.yml +++ b/tests/modules/nf-core/deepvariant/test.yml @@ -1,5 +1,5 @@ - name: deepvariant test_deepvariant - command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant -c ./tests/config/nextflow.config tags: - deepvariant files: @@ -11,7 +11,7 @@ md5sum: 51572055ca5c07fc4001b25a9c273bf8 - name: deepvariant test_deepvariant_cram_intervals - command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant_cram_intervals -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/deepvariant -entry test_deepvariant_cram_intervals -c ./tests/config/nextflow.config tags: - deepvariant files: diff --git a/tests/modules/nf-core/diamond/blastp/test.yml b/tests/modules/nf-core/diamond/blastp/test.yml index 73e983cf8cf..910a464c43d 100644 --- a/tests/modules/nf-core/diamond/blastp/test.yml +++ b/tests/modules/nf-core/diamond/blastp/test.yml @@ -1,5 +1,5 @@ - name: diamond blastp test_diamond_blastp - command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config tags: - diamond/blastp - diamond @@ -8,7 +8,7 @@ - path: output/diamond/versions.yml - name: diamond blastp test_diamond_blastp_daa - command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/blastp -entry test_diamond_blastp_daa -c ./tests/config/nextflow.config tags: - diamond/blastp - diamond diff --git a/tests/modules/nf-core/diamond/makedb/test.yml b/tests/modules/nf-core/diamond/makedb/test.yml index 5631872e133..e62ccc2c8eb 100644 --- a/tests/modules/nf-core/diamond/makedb/test.yml +++ b/tests/modules/nf-core/diamond/makedb/test.yml @@ -1,5 +1,5 @@ - name: diamond makedb test_diamond_makedb - command: nextflow run ./tests/modules/nf-core/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config tags: - diamond/makedb - diamond diff --git a/tests/modules/nf-core/elprep/filter/test.yml b/tests/modules/nf-core/elprep/filter/test.yml index 835febf5c51..8425e30406c 100644 --- a/tests/modules/nf-core/elprep/filter/test.yml +++ b/tests/modules/nf-core/elprep/filter/test.yml @@ -1,5 +1,5 @@ - name: elprep filter test_elprep_filter - command: nextflow run ./tests/modules/nf-core/elprep/filter -entry test_elprep_filter -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/elprep/filter -entry test_elprep_filter -c ./tests/config/nextflow.config tags: - elprep - elprep/filter diff --git a/tests/modules/nf-core/elprep/merge/test.yml b/tests/modules/nf-core/elprep/merge/test.yml index 11560b284cb..a0b95b8d0bf 100644 --- a/tests/modules/nf-core/elprep/merge/test.yml +++ b/tests/modules/nf-core/elprep/merge/test.yml @@ -1,5 +1,5 @@ - name: elprep merge test_elprep_merge - command: nextflow run ./tests/modules/nf-core/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config tags: - elprep - elprep/merge diff --git a/tests/modules/nf-core/elprep/split/test.yml b/tests/modules/nf-core/elprep/split/test.yml index 382e0dd4adc..cda8d91ec4d 100644 --- a/tests/modules/nf-core/elprep/split/test.yml +++ b/tests/modules/nf-core/elprep/split/test.yml @@ -1,5 +1,5 @@ - name: elprep split test_elprep_split - command: nextflow run ./tests/modules/nf-core/elprep/split -entry test_elprep_split -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/elprep/split -entry test_elprep_split -c ./tests/config/nextflow.config tags: - elprep - elprep/split diff --git a/tests/modules/nf-core/faqcs/test.yml b/tests/modules/nf-core/faqcs/test.yml index 43023a8937f..1a06fab7af2 100644 --- a/tests/modules/nf-core/faqcs/test.yml +++ b/tests/modules/nf-core/faqcs/test.yml @@ -1,5 +1,5 @@ - name: faqcs test_fastp_single_end - command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_single_end -c ./tests/config/nextflow.config tags: - faqcs files: @@ -26,7 +26,7 @@ md5sum: 2a38d7e7ab5299336e9669c393c9da6c - name: faqcs test_fastp_paired_end - command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/faqcs -entry test_fastp_paired_end -c ./tests/config/nextflow.config tags: - faqcs files: diff --git a/tests/modules/nf-core/freebayes/test.yml b/tests/modules/nf-core/freebayes/test.yml index e2c3df624df..6148591bd82 100644 --- a/tests/modules/nf-core/freebayes/test.yml +++ b/tests/modules/nf-core/freebayes/test.yml @@ -1,5 +1,5 @@ - name: freebayes test_freebayes - command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes -c ./tests/config/nextflow.config tags: - freebayes files: @@ -9,7 +9,7 @@ md5sum: 53651eb835af65df829241257584a7d2 - name: freebayes test_freebayes_bed - command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config tags: - freebayes files: @@ -19,7 +19,7 @@ md5sum: becc93c8a0be580c09d55b955d60a5e1 - name: freebayes test_freebayes_cram - command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config tags: - freebayes files: @@ -29,7 +29,7 @@ md5sum: 2e5b266edfc6cab81353cfc72c00f67c - name: freebayes test_freebayes_somatic - command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config tags: - freebayes files: @@ -39,7 +39,7 @@ md5sum: 8fbdb4c052fb3e42b5508a966125fa05 - name: freebayes test_freebayes_somatic_cram_intervals - command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config tags: - freebayes files: diff --git a/tests/modules/nf-core/gamma/gamma/test.yml b/tests/modules/nf-core/gamma/gamma/test.yml index 9b86a6a8bdb..3b15296d9ac 100644 --- a/tests/modules/nf-core/gamma/gamma/test.yml +++ b/tests/modules/nf-core/gamma/gamma/test.yml @@ -1,5 +1,5 @@ - name: gamma gamma test_unzip - command: nextflow run ./tests/modules/nf-core/gamma/gamma -entry test_unzip -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gamma/gamma -entry test_unzip -c ./tests/config/nextflow.config tags: - gamma/gamma - gamma @@ -14,7 +14,7 @@ md5sum: 8baafec7b3b87f788f69e30d317c9722 - name: gamma gamma test_gamma - command: nextflow run ./tests/modules/nf-core/gamma/gamma -entry test_gamma -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gamma/gamma -entry test_gamma -c ./tests/config/nextflow.config tags: - gamma/gamma - gamma diff --git a/tests/modules/nf-core/gatk4/applybqsr/test.yml b/tests/modules/nf-core/gatk4/applybqsr/test.yml index 032b43f863b..9821c649384 100644 --- a/tests/modules/nf-core/gatk4/applybqsr/test.yml +++ b/tests/modules/nf-core/gatk4/applybqsr/test.yml @@ -1,5 +1,5 @@ - name: gatk4 applybqsr test_gatk4_applybqsr - command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config tags: - gatk4 - gatk4/applybqsr @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 applybqsr test_gatk4_applybqsr_intervals - command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config tags: - gatk4 - gatk4/applybqsr @@ -19,7 +19,7 @@ - path: output/gatk4/versions.yml - name: gatk4 applybqsr test_gatk4_applybqsr_cram - command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsr/nextflow.config tags: - gatk4 - gatk4/applybqsr diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/test.yml b/tests/modules/nf-core/gatk4/applybqsrspark/test.yml index 5283e2c4ad2..fdffc886608 100644 --- a/tests/modules/nf-core/gatk4/applybqsrspark/test.yml +++ b/tests/modules/nf-core/gatk4/applybqsrspark/test.yml @@ -1,5 +1,5 @@ - name: gatk4 applybqsr test_gatk4_applybqsr_spark - command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config tags: - gatk4 - gatk4/applybqsrspark @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals - command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_intervals -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config tags: - gatk4 - gatk4/applybqsrspark @@ -18,7 +18,7 @@ - path: output/gatk4/versions.yml - name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram - command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_cram -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applybqsrspark -entry test_gatk4_applybqsr_spark_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applybqsrspark/nextflow.config tags: - gatk4 - gatk4/applybqsrspark diff --git a/tests/modules/nf-core/gatk4/applyvqsr/test.yml b/tests/modules/nf-core/gatk4/applyvqsr/test.yml index d81535deeb0..63e5ceba396 100644 --- a/tests/modules/nf-core/gatk4/applyvqsr/test.yml +++ b/tests/modules/nf-core/gatk4/applyvqsr/test.yml @@ -1,5 +1,5 @@ - name: gatk4 applyvqsr test_gatk4_applyvqsr - command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config tags: - gatk4/applyvqsr - gatk4 @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific - command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config tags: - gatk4/applyvqsr - gatk4 diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/test.yml b/tests/modules/nf-core/gatk4/calculatecontamination/test.yml index 3c492fec093..a673dd68cf1 100644 --- a/tests/modules/nf-core/gatk4/calculatecontamination/test.yml +++ b/tests/modules/nf-core/gatk4/calculatecontamination/test.yml @@ -1,5 +1,5 @@ - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only - command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config tags: - gatk4 - gatk4/calculatecontamination @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair - command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config tags: - gatk4 - gatk4/calculatecontamination @@ -19,7 +19,7 @@ - path: output/gatk4/versions.yml - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation - command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config tags: - gatk4 - gatk4/calculatecontamination diff --git a/tests/modules/nf-core/gatk4/combinegvcfs/test.yml b/tests/modules/nf-core/gatk4/combinegvcfs/test.yml index 13297f0bf55..7ad0610f2b7 100644 --- a/tests/modules/nf-core/gatk4/combinegvcfs/test.yml +++ b/tests/modules/nf-core/gatk4/combinegvcfs/test.yml @@ -1,5 +1,5 @@ - name: gatk4 combinegvcfs test_gatk4_combinegvcfs - command: nextflow run ./tests/modules/nf-core/gatk4/combinegvcfs -entry test_gatk4_combinegvcfs -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/combinegvcfs -entry test_gatk4_combinegvcfs -c ./tests/config/nextflow.config tags: - gatk4 - gatk4/combinegvcfs diff --git a/tests/modules/nf-core/gatk4/fastqtosam/test.yml b/tests/modules/nf-core/gatk4/fastqtosam/test.yml index 874be4e1a30..e4932ebf135 100644 --- a/tests/modules/nf-core/gatk4/fastqtosam/test.yml +++ b/tests/modules/nf-core/gatk4/fastqtosam/test.yml @@ -1,5 +1,5 @@ - name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end - command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config tags: - gatk4 - gatk4/fastqtosam @@ -8,7 +8,7 @@ - path: output/gatk4/versions.yml - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end - command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config tags: - gatk4 - gatk4/fastqtosam diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml b/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml index 857a8033e91..e70c49eaa86 100644 --- a/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml +++ b/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml @@ -1,5 +1,5 @@ - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports - command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c ./tests/config/nextflow.config tags: - gatk4 - gatk4/gatherbqsrreports @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple - command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c ./tests/config/nextflow.config tags: - gatk4 - gatk4/gatherbqsrreports diff --git a/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml b/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml index c0417e4435f..5a972c8bbe1 100644 --- a/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml +++ b/tests/modules/nf-core/gatk4/genomicsdbimport/test.yml @@ -1,5 +1,5 @@ - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_create_genomicsdb - command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config tags: - gatk4 - gatk4/genomicsdbimport @@ -19,7 +19,7 @@ - path: output/gatk4/versions.yml - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist - command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config tags: - gatk4 - gatk4/genomicsdbimport @@ -30,7 +30,7 @@ - path: output/untar/versions.yml - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_update_genomicsdb - command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genomicsdbimport/nextflow.config tags: - gatk4 - gatk4/genomicsdbimport diff --git a/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml b/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml index ee37c3d39d8..b727ff4d269 100644 --- a/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml +++ b/tests/modules/nf-core/gatk4/getpileupsummaries/test.yml @@ -1,5 +1,5 @@ - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites - command: nextflow run ./tests/modules/nf-core/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config tags: - gatk4/getpileupsummaries - gatk4 @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram - command: nextflow run ./tests/modules/nf-core/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c ./tests/config/nextflow.config tags: - gatk4/getpileupsummaries - gatk4 diff --git a/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml b/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml index 50d77763a6d..3e7483a2e6d 100644 --- a/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml +++ b/tests/modules/nf-core/gatk4/indexfeaturefile/test.yml @@ -1,5 +1,5 @@ - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed - command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config tags: - gatk4 - gatk4/indexfeaturefile @@ -8,7 +8,7 @@ - path: output/gatk4/versions.yml - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz - command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config tags: - gatk4 - gatk4/indexfeaturefile @@ -18,7 +18,7 @@ - path: output/gatk4/versions.yml - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf - command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/indexfeaturefile/nextflow.config tags: - gatk4 - gatk4/indexfeaturefile @@ -27,7 +27,7 @@ - path: output/gatk4/versions.yml - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz - command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c ./tests/config/nextflow.config tags: - gatk4 - gatk4/indexfeaturefile diff --git a/tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config b/tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config index e0455b4be19..1b948a6aa39 100644 --- a/tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config +++ b/tests/modules/nf-core/gatk4/markduplicatesspark/nextflow.config @@ -14,6 +14,6 @@ process { } } -// override tests/config/nextflow.config +// override ./tests/config/nextflow.config docker.userEmulation = false diff --git a/tests/modules/nf-core/gatk4/selectvariants/test.yml b/tests/modules/nf-core/gatk4/selectvariants/test.yml index 7dbda19a9fa..ad6568ddf60 100644 --- a/tests/modules/nf-core/gatk4/selectvariants/test.yml +++ b/tests/modules/nf-core/gatk4/selectvariants/test.yml @@ -1,5 +1,5 @@ - name: gatk4 selectvariants test_gatk4_selectvariants_vcf_input - command: nextflow run ./tests/modules/nf-core/gatk4/selectvariants -entry test_gatk4_selectvariants_vcf_input -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/selectvariants -entry test_gatk4_selectvariants_vcf_input -c ./tests/config/nextflow.config tags: - gatk4/selectvariants - gatk4 @@ -9,7 +9,7 @@ - path: output/gatk4/versions.yml - name: gatk4 selectvariants test_gatk4_selectvariants_gz_input - command: nextflow run ./tests/modules/nf-core/gatk4/selectvariants -entry test_gatk4_selectvariants_gz_input -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/selectvariants -entry test_gatk4_selectvariants_gz_input -c ./tests/config/nextflow.config tags: - gatk4/selectvariants - gatk4 diff --git a/tests/modules/nf-core/gatk4/splitintervals/test.yml b/tests/modules/nf-core/gatk4/splitintervals/test.yml index 481035c7412..1230731471f 100644 --- a/tests/modules/nf-core/gatk4/splitintervals/test.yml +++ b/tests/modules/nf-core/gatk4/splitintervals/test.yml @@ -1,5 +1,5 @@ - name: gatk4 splitintervals test_gatk4_splitintervals_bed - command: nextflow run ./tests/modules/nf-core/gatk4/splitintervals -entry test_gatk4_splitintervals_bed -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/splitintervals -entry test_gatk4_splitintervals_bed -c ./tests/config/nextflow.config tags: - gatk4/splitintervals - gatk4 @@ -11,7 +11,7 @@ - path: output/gatk4/versions.yml - name: gatk4 splitintervals test_gatk4_splitintervals_intervals - command: nextflow run ./tests/modules/nf-core/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/splitintervals -entry test_gatk4_splitintervals_intervals -c ./tests/config/nextflow.config tags: - gatk4/splitintervals - gatk4 diff --git a/tests/modules/nf-core/gatk4/splitncigarreads/test.yml b/tests/modules/nf-core/gatk4/splitncigarreads/test.yml index 041d5ebd8a2..1fcf4de65bd 100644 --- a/tests/modules/nf-core/gatk4/splitncigarreads/test.yml +++ b/tests/modules/nf-core/gatk4/splitncigarreads/test.yml @@ -1,5 +1,5 @@ - name: gatk4 splitncigarreads test_gatk4_splitncigarreads - command: nextflow run ./tests/modules/nf-core/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c ./tests/config/nextflow.config tags: - gatk4 - gatk4/splitncigarreads @@ -8,7 +8,7 @@ md5sum: 37e5dbce8692b54c3292b539c91dfbd7 - path: output/gatk4/versions.yml - name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals - command: nextflow run ./tests/modules/nf-core/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c ./tests/config/nextflow.config tags: - gatk4 - gatk4/splitncigarreads diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml b/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml index fba60c188c2..b24b45cbe13 100644 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml +++ b/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml @@ -1,5 +1,5 @@ - name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator - command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config tags: - gatk4 - gatk4/variantrecalibrator @@ -13,7 +13,7 @@ - path: output/gatk4/versions.yml - name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific - command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator_allele_specific -c tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config + command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config tags: - gatk4 - gatk4/variantrecalibrator diff --git a/tests/modules/nf-core/genomescope2/test.yml b/tests/modules/nf-core/genomescope2/test.yml index 0516830c570..cb6a1fb6fcc 100644 --- a/tests/modules/nf-core/genomescope2/test.yml +++ b/tests/modules/nf-core/genomescope2/test.yml @@ -1,5 +1,5 @@ - name: genomescope2 test_genomescope2 - command: nextflow run ./tests/modules/nf-core/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/genomescope2 -entry test_genomescope2 -c ./tests/config/nextflow.config tags: - genomescope2 files: diff --git a/tests/modules/nf-core/gstama/polyacleanup/test.yml b/tests/modules/nf-core/gstama/polyacleanup/test.yml index b1c97224f1f..6a1ed064c0e 100644 --- a/tests/modules/nf-core/gstama/polyacleanup/test.yml +++ b/tests/modules/nf-core/gstama/polyacleanup/test.yml @@ -1,5 +1,5 @@ - name: gstama polyacleanup test_gstama_polyacleanup - command: nextflow run ./tests/modules/nf-core/gstama/polyacleanup -entry test_gstama_polyacleanup -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/gstama/polyacleanup -entry test_gstama_polyacleanup -c ./tests/config/nextflow.config tags: - gstama - gstama/polyacleanup diff --git a/tests/modules/nf-core/hamronization/deeparg/test.yml b/tests/modules/nf-core/hamronization/deeparg/test.yml index 61b0ac7de10..f5a2ce83b24 100644 --- a/tests/modules/nf-core/hamronization/deeparg/test.yml +++ b/tests/modules/nf-core/hamronization/deeparg/test.yml @@ -1,5 +1,5 @@ - name: hamronization deeparg test_hamronization_deeparg - command: nextflow run ./tests/modules/nf-core/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hamronization/deeparg -entry test_hamronization_deeparg -c ./tests/config/nextflow.config tags: - hamronization - hamronization/deeparg diff --git a/tests/modules/nf-core/happy/happy/test.yml b/tests/modules/nf-core/happy/happy/test.yml index 1b394275c34..f0bcc1cf66d 100644 --- a/tests/modules/nf-core/happy/happy/test.yml +++ b/tests/modules/nf-core/happy/happy/test.yml @@ -1,5 +1,5 @@ - name: happy happy test_happy_vcf - command: nextflow run ./tests/modules/nf-core/happy/happy -entry test_happy_vcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/happy/happy -entry test_happy_vcf -c ./tests/config/nextflow.config tags: - happy - happy/happy @@ -13,7 +13,7 @@ md5sum: 82243bf6dbdc71aa63211ee2a89f47f2 - name: happy happy test_happy_gvcf - command: nextflow run ./tests/modules/nf-core/happy/happy -entry test_happy_gvcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/happy/happy -entry test_happy_gvcf -c ./tests/config/nextflow.config tags: - happy - happy/happy diff --git a/tests/modules/nf-core/happy/prepy/test.yml b/tests/modules/nf-core/happy/prepy/test.yml index 2ec6141e7a1..fd929d83277 100644 --- a/tests/modules/nf-core/happy/prepy/test.yml +++ b/tests/modules/nf-core/happy/prepy/test.yml @@ -1,5 +1,5 @@ - name: happy prepy test_happy_prepy_vcf - command: nextflow run ./tests/modules/nf-core/happy/prepy -entry test_happy_prepy_vcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/happy/prepy -entry test_happy_prepy_vcf -c ./tests/config/nextflow.config tags: - happy/prepy - happy @@ -9,7 +9,7 @@ md5sum: 814d20f1f29f23a3d21012748a5d6393 - name: happy prepy test_happy_prepy_gvcf - command: nextflow run ./tests/modules/nf-core/happy/prepy -entry test_happy_prepy_gvcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/happy/prepy -entry test_happy_prepy_gvcf -c ./tests/config/nextflow.config tags: - happy/prepy - happy diff --git a/tests/modules/nf-core/hmmcopy/generatemap/test.yml b/tests/modules/nf-core/hmmcopy/generatemap/test.yml index 21c97e122e8..ef45a71782c 100644 --- a/tests/modules/nf-core/hmmcopy/generatemap/test.yml +++ b/tests/modules/nf-core/hmmcopy/generatemap/test.yml @@ -1,5 +1,5 @@ - name: hmmcopy generatemap test_hmmcopy_generatemap - command: nextflow run ./tests/modules/nf-core/hmmcopy/generatemap -entry test_hmmcopy_generatemap -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hmmcopy/generatemap -entry test_hmmcopy_generatemap -c ./tests/config/nextflow.config tags: - hmmcopy - hmmcopy/generatemap diff --git a/tests/modules/nf-core/hmmcopy/mapcounter/test.yml b/tests/modules/nf-core/hmmcopy/mapcounter/test.yml index fdb8c174088..dd8d1336b54 100644 --- a/tests/modules/nf-core/hmmcopy/mapcounter/test.yml +++ b/tests/modules/nf-core/hmmcopy/mapcounter/test.yml @@ -1,5 +1,5 @@ - name: hmmcopy mapcounter test_hmmcopy_mapcounter - command: nextflow run ./tests/modules/nf-core/hmmcopy/mapcounter -entry test_hmmcopy_mapcounter -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hmmcopy/mapcounter -entry test_hmmcopy_mapcounter -c ./tests/config/nextflow.config tags: - hmmcopy/mapcounter - hmmcopy diff --git a/tests/modules/nf-core/hmmcopy/readcounter/test.yml b/tests/modules/nf-core/hmmcopy/readcounter/test.yml index 6b0c81870f9..8184e7c1552 100644 --- a/tests/modules/nf-core/hmmcopy/readcounter/test.yml +++ b/tests/modules/nf-core/hmmcopy/readcounter/test.yml @@ -1,5 +1,5 @@ - name: hmmcopy readcounter test_hmmcopy_readcounter - command: nextflow run ./tests/modules/nf-core/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c ./tests/config/nextflow.config tags: - hmmcopy - hmmcopy/readcounter diff --git a/tests/modules/nf-core/hmmer/eslalimask/main.nf b/tests/modules/nf-core/hmmer/eslalimask/main.nf index c84ba730b26..1213f09d956 100644 --- a/tests/modules/nf-core/hmmer/eslalimask/main.nf +++ b/tests/modules/nf-core/hmmer/eslalimask/main.nf @@ -9,7 +9,7 @@ workflow test_hmmer_rfmask { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz') diff --git a/tests/modules/nf-core/hmmer/eslreformat/main.nf b/tests/modules/nf-core/hmmer/eslreformat/main.nf index a70c318227f..bef217f544d 100644 --- a/tests/modules/nf-core/hmmer/eslreformat/main.nf +++ b/tests/modules/nf-core/hmmer/eslreformat/main.nf @@ -11,7 +11,7 @@ workflow test_hmmer_eslreformat_afa { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz') @@ -25,7 +25,7 @@ workflow test_hmmer_eslreformat_phylip { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz') @@ -39,7 +39,7 @@ workflow test_hmmer_eslreformat_unalign { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz') diff --git a/tests/modules/nf-core/hmmer/hmmalign/main.nf b/tests/modules/nf-core/hmmer/hmmalign/main.nf index 08d8717750b..e5d8e3b6c80 100644 --- a/tests/modules/nf-core/hmmer/hmmalign/main.nf +++ b/tests/modules/nf-core/hmmer/hmmalign/main.nf @@ -9,7 +9,7 @@ workflow test_hmmer_hmmalign { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz') @@ -21,7 +21,7 @@ workflow test_hmmer_hmmalign_prefix { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz') diff --git a/tests/modules/nf-core/hmmer/hmmsearch/test.yml b/tests/modules/nf-core/hmmer/hmmsearch/test.yml index cef7581e09f..8e6ddcd7ae1 100644 --- a/tests/modules/nf-core/hmmer/hmmsearch/test.yml +++ b/tests/modules/nf-core/hmmer/hmmsearch/test.yml @@ -1,5 +1,5 @@ - name: hmmer hmmsearch test_hmmer_hmmsearch - command: nextflow run ./tests/modules/nf-core/hmmer/hmmsearch -entry test_hmmer_hmmsearch -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hmmer/hmmsearch -entry test_hmmer_hmmsearch -c ./tests/config/nextflow.config tags: - hmmer/hmmsearch - hmmer @@ -11,7 +11,7 @@ md5sum: ed0808c10abd205c6bd0fb01f45259bb - name: hmmer hmmsearch test_hmmer_hmmsearch_optional - command: nextflow run ./tests/modules/nf-core/hmmer/hmmsearch -entry test_hmmer_hmmsearch_optional -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hmmer/hmmsearch -entry test_hmmer_hmmsearch_optional -c ./tests/config/nextflow.config tags: - hmmer/hmmsearch - hmmer diff --git a/tests/modules/nf-core/hpsuissero/test.yml b/tests/modules/nf-core/hpsuissero/test.yml index aae4993d771..f4a88f76abf 100644 --- a/tests/modules/nf-core/hpsuissero/test.yml +++ b/tests/modules/nf-core/hpsuissero/test.yml @@ -1,5 +1,5 @@ - name: hpsuissero test_hpsuissero - command: nextflow run ./tests/modules/nf-core/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/hpsuissero -entry test_hpsuissero -c ./tests/config/nextflow.config tags: - hpsuissero files: diff --git a/tests/modules/nf-core/ichorcna/createpon/test.yml b/tests/modules/nf-core/ichorcna/createpon/test.yml index 9a043f3dbd1..a4352ad5c09 100644 --- a/tests/modules/nf-core/ichorcna/createpon/test.yml +++ b/tests/modules/nf-core/ichorcna/createpon/test.yml @@ -1,5 +1,5 @@ - name: ichorcna createpon test_ichorcna_createpon - command: nextflow run ./tests/modules/nf-core/ichorcna/createpon -entry test_ichorcna_createpon -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ichorcna/createpon -entry test_ichorcna_createpon -c ./tests/config/nextflow.config tags: - ichorcna/createpon - ichorcna @@ -10,7 +10,7 @@ md5sum: 59a2121301113cc013bfae65935e07f1 - name: ichorcna createpon test_ichorcna_createpon2 - command: nextflow run ./tests/modules/nf-core/ichorcna/createpon -entry test_ichorcna_createpon2 -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ichorcna/createpon -entry test_ichorcna_createpon2 -c ./tests/config/nextflow.config tags: - ichorcna/createpon - ichorcna diff --git a/tests/modules/nf-core/ichorcna/run/test.yml b/tests/modules/nf-core/ichorcna/run/test.yml index 4708326eacc..963cae64906 100644 --- a/tests/modules/nf-core/ichorcna/run/test.yml +++ b/tests/modules/nf-core/ichorcna/run/test.yml @@ -1,5 +1,5 @@ - name: ichorcna run test_ichorcna_run_no_panel - command: nextflow run ./tests/modules/nf-core/ichorcna/run -entry test_ichorcna_run_no_panel -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ichorcna/run -entry test_ichorcna_run_no_panel -c ./tests/config/nextflow.config tags: - ichorcna - ichorcna/run @@ -12,7 +12,7 @@ md5sum: effb37e19bec3609417aaccad4b6a294 - name: ichorcna run test_ichorcna_run_inc_panel - command: nextflow run ./tests/modules/nf-core/ichorcna/run -entry test_ichorcna_run_inc_panel -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ichorcna/run -entry test_ichorcna_run_inc_panel -c ./tests/config/nextflow.config tags: - ichorcna - ichorcna/run diff --git a/tests/modules/nf-core/kaiju/kaiju/test.yml b/tests/modules/nf-core/kaiju/kaiju/test.yml index b30f0322e46..9e495ede0b0 100644 --- a/tests/modules/nf-core/kaiju/kaiju/test.yml +++ b/tests/modules/nf-core/kaiju/kaiju/test.yml @@ -1,5 +1,5 @@ - name: kaiju kaiju test_kaiju_kaiju_single_end - command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_single_end -c ./tests/config/nextflow.config tags: - kaiju/kaiju - kaiju @@ -10,7 +10,7 @@ md5sum: 7e218c0ea00a71dd3a5ec5aaf28804f4 - name: kaiju kaiju test_kaiju_kaiju_paired_end - command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_paired_end -c ./tests/config/nextflow.config tags: - kaiju/kaiju - kaiju diff --git a/tests/modules/nf-core/kaiju/kaiju2table/test.yml b/tests/modules/nf-core/kaiju/kaiju2table/test.yml index d38f804bf8b..aeb1fd57d75 100644 --- a/tests/modules/nf-core/kaiju/kaiju2table/test.yml +++ b/tests/modules/nf-core/kaiju/kaiju2table/test.yml @@ -1,5 +1,5 @@ - name: kaiju kaiju2table test_kaiju_kaiju_single_end - command: nextflow run ./tests/modules/nf-core/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c ./tests/config/nextflow.config tags: - kaiju - kaiju/kaiju2table diff --git a/tests/modules/nf-core/kat/hist/test.yml b/tests/modules/nf-core/kat/hist/test.yml index 9236f03857a..640716e56a2 100644 --- a/tests/modules/nf-core/kat/hist/test.yml +++ b/tests/modules/nf-core/kat/hist/test.yml @@ -1,5 +1,5 @@ - name: kat hist test_kat_hist_single_end - command: nextflow run ./tests/modules/nf-core/kat/hist -entry test_kat_hist_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kat/hist -entry test_kat_hist_single_end -c ./tests/config/nextflow.config tags: - kat/hist - kat @@ -21,7 +21,7 @@ - path: output/kat/versions.yml - name: kat hist test_kat_hist_paired_end - command: nextflow run ./tests/modules/nf-core/kat/hist -entry test_kat_hist_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kat/hist -entry test_kat_hist_paired_end -c ./tests/config/nextflow.config tags: - kat/hist - kat diff --git a/tests/modules/nf-core/kraken2/kraken2/test.yml b/tests/modules/nf-core/kraken2/kraken2/test.yml index 39f52219391..595647ba379 100644 --- a/tests/modules/nf-core/kraken2/kraken2/test.yml +++ b/tests/modules/nf-core/kraken2/kraken2/test.yml @@ -1,5 +1,5 @@ - name: kraken2 kraken2 test_kraken2_kraken2_single_end - command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c ./tests/config/nextflow.config tags: - kraken2 - kraken2/kraken2 @@ -13,7 +13,7 @@ - path: output/untar/versions.yml - name: kraken2 kraken2 test_kraken2_kraken2_paired_end - command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c ./tests/config/nextflow.config tags: - kraken2 - kraken2/kraken2 @@ -29,7 +29,7 @@ - path: output/untar/versions.yml - name: kraken2 kraken2 test_kraken2_kraken2_classifyreads - command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_classifyreads -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/kraken2/kraken2 -entry test_kraken2_kraken2_classifyreads -c ./tests/config/nextflow.config tags: - kraken2 - kraken2/kraken2 diff --git a/tests/modules/nf-core/krona/ktimporttext/test.yml b/tests/modules/nf-core/krona/ktimporttext/test.yml index dd02a863e83..ff93014974c 100644 --- a/tests/modules/nf-core/krona/ktimporttext/test.yml +++ b/tests/modules/nf-core/krona/ktimporttext/test.yml @@ -1,5 +1,5 @@ - name: krona ktimporttext test_krona_ktimporttext_multi - command: nextflow run ./tests/modules/nf-core/krona/ktimporttext -entry test_krona_ktimporttext_multi -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/krona/ktimporttext -entry test_krona_ktimporttext_multi -c ./tests/config/nextflow.config tags: - krona - krona/ktimporttext @@ -9,7 +9,7 @@ - "DOCTYPE html PUBLIC" - name: krona ktimporttext test_krona_ktimporttext_single - command: nextflow run ./tests/modules/nf-core/krona/ktimporttext -entry test_krona_ktimporttext_single -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/krona/ktimporttext -entry test_krona_ktimporttext_single -c ./tests/config/nextflow.config tags: - krona - krona/ktimporttext diff --git a/tests/modules/nf-core/legsta/test.yml b/tests/modules/nf-core/legsta/test.yml index b181e664732..6d193422d34 100644 --- a/tests/modules/nf-core/legsta/test.yml +++ b/tests/modules/nf-core/legsta/test.yml @@ -1,5 +1,5 @@ - name: legsta test_legsta - command: nextflow run ./tests/modules/nf-core/legsta -entry test_legsta -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/legsta -entry test_legsta -c ./tests/config/nextflow.config tags: - legsta files: diff --git a/tests/modules/nf-core/mafft/test.yml b/tests/modules/nf-core/mafft/test.yml index b29d63d242f..1d3bb3b15a0 100644 --- a/tests/modules/nf-core/mafft/test.yml +++ b/tests/modules/nf-core/mafft/test.yml @@ -1,5 +1,5 @@ - name: mafft test_mafft - command: nextflow run ./tests/modules/nf-core/mafft -entry test_mafft -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/mafft -entry test_mafft -c ./tests/config/nextflow.config tags: - mafft files: diff --git a/tests/modules/nf-core/mash/dist/test.yml b/tests/modules/nf-core/mash/dist/test.yml index 7d279e4b7c9..27fd099c3cf 100644 --- a/tests/modules/nf-core/mash/dist/test.yml +++ b/tests/modules/nf-core/mash/dist/test.yml @@ -1,5 +1,5 @@ - name: mash dist test_mash_dist - command: nextflow run ./tests/modules/nf-core/mash/dist -entry test_mash_dist -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/mash/dist -entry test_mash_dist -c ./tests/config/nextflow.config tags: - mash - mash/dist diff --git a/tests/modules/nf-core/maxquant/lfq/test.yml b/tests/modules/nf-core/maxquant/lfq/test.yml index bce6864fb43..fd2cf9a7fac 100644 --- a/tests/modules/nf-core/maxquant/lfq/test.yml +++ b/tests/modules/nf-core/maxquant/lfq/test.yml @@ -1,5 +1,5 @@ - name: maxquant lfq - command: nextflow run ./tests/modules/nf-core/maxquant/lfq -entry test_maxquant_lfq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/maxquant/lfq -entry test_maxquant_lfq -c ./tests/config/nextflow.config tags: - maxquant - maxquant/lfq diff --git a/tests/modules/nf-core/md5sum/test.yml b/tests/modules/nf-core/md5sum/test.yml index fdddeb2163f..02b8efe5a28 100644 --- a/tests/modules/nf-core/md5sum/test.yml +++ b/tests/modules/nf-core/md5sum/test.yml @@ -1,5 +1,5 @@ - name: md5sum test_md5sum - command: nextflow run ./tests/modules/nf-core/md5sum -entry test_md5sum -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/md5sum -entry test_md5sum -c ./tests/config/nextflow.config tags: - md5sum files: diff --git a/tests/modules/nf-core/megan/rma2info/test.yml b/tests/modules/nf-core/megan/rma2info/test.yml index c8d9f25dbc4..dd39a159da8 100644 --- a/tests/modules/nf-core/megan/rma2info/test.yml +++ b/tests/modules/nf-core/megan/rma2info/test.yml @@ -1,5 +1,5 @@ - name: megan rma2info test_megan_rma2info - command: nextflow run ./tests/modules/nf-core/megan/rma2info -entry test_megan_rma2info -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/megan/rma2info -entry test_megan_rma2info -c ./tests/config/nextflow.config tags: - megan - megan/rma2info diff --git a/tests/modules/nf-core/meryl/count/test.yml b/tests/modules/nf-core/meryl/count/test.yml index f95d559b01d..7f4f9a50aac 100644 --- a/tests/modules/nf-core/meryl/count/test.yml +++ b/tests/modules/nf-core/meryl/count/test.yml @@ -1,5 +1,5 @@ - name: meryl count test_meryl_count_single_end - command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_single_end -c ./tests/config/nextflow.config tags: - meryl/count - meryl @@ -8,7 +8,7 @@ md5sum: 5fe537d873925ccbcc4edf0983e9eda0 - name: meryl count test_meryl_count_paired_end - command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_paired_end -c ./tests/config/nextflow.config tags: - meryl/count - meryl diff --git a/tests/modules/nf-core/meryl/histogram/test.yml b/tests/modules/nf-core/meryl/histogram/test.yml index f32200e23cf..7d794aa773b 100644 --- a/tests/modules/nf-core/meryl/histogram/test.yml +++ b/tests/modules/nf-core/meryl/histogram/test.yml @@ -1,5 +1,5 @@ - name: meryl histogram test_meryl_histogram - command: nextflow run ./tests/modules/nf-core/meryl/histogram -entry test_meryl_histogram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/meryl/histogram -entry test_meryl_histogram -c ./tests/config/nextflow.config tags: - meryl/histogram - meryl diff --git a/tests/modules/nf-core/meryl/unionsum/test.yml b/tests/modules/nf-core/meryl/unionsum/test.yml index a93ba9732c3..244b2a58644 100644 --- a/tests/modules/nf-core/meryl/unionsum/test.yml +++ b/tests/modules/nf-core/meryl/unionsum/test.yml @@ -1,5 +1,5 @@ - name: meryl unionsum test_meryl_unionsum_single_end - command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_single_end -c ./tests/config/nextflow.config tags: - meryl - meryl/unionsum @@ -8,7 +8,7 @@ md5sum: 7de859c6d3a29d72f6c9c976609d0913 - name: meryl unionsum test_meryl_unionsum_paired_end - command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_paired_end -c ./tests/config/nextflow.config tags: - meryl - meryl/unionsum diff --git a/tests/modules/nf-core/metabat2/metabat2/test.yml b/tests/modules/nf-core/metabat2/metabat2/test.yml index 167708a9881..e1766921426 100644 --- a/tests/modules/nf-core/metabat2/metabat2/test.yml +++ b/tests/modules/nf-core/metabat2/metabat2/test.yml @@ -1,5 +1,5 @@ - name: metabat2 metabat2 test_metabat2_no_depth - command: nextflow run ./tests/modules/nf-core/metabat2/metabat2 -entry test_metabat2_no_depth -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/metabat2/metabat2 -entry test_metabat2_no_depth -c ./tests/config/nextflow.config tags: - metabat2 - metabat2/metabat2 @@ -11,7 +11,7 @@ md5sum: 5742a71af36c3a748fd5726d76924ba8 - name: metabat2 metabat2 test_metabat2_depth - command: nextflow run ./tests/modules/nf-core/metabat2/metabat2 -entry test_metabat2_depth -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/metabat2/metabat2 -entry test_metabat2_depth -c ./tests/config/nextflow.config tags: - metabat2 - metabat2/metabat2 diff --git a/tests/modules/nf-core/minimap2/align/test.yml b/tests/modules/nf-core/minimap2/align/test.yml index 8fd0b3e1e99..178c23a1c72 100644 --- a/tests/modules/nf-core/minimap2/align/test.yml +++ b/tests/modules/nf-core/minimap2/align/test.yml @@ -1,5 +1,5 @@ - name: minimap2 align test_minimap2_align_single_end - command: nextflow run ./tests/modules/nf-core/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config tags: - minimap2 - minimap2/align @@ -8,7 +8,7 @@ - path: output/minimap2/versions.yml - name: minimap2 align test_minimap2_align_paired_end - command: nextflow run ./tests/modules/nf-core/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config tags: - minimap2 - minimap2/align diff --git a/tests/modules/nf-core/mobsuite/recon/test.yml b/tests/modules/nf-core/mobsuite/recon/test.yml index b7014b59841..47cfd00ed31 100644 --- a/tests/modules/nf-core/mobsuite/recon/test.yml +++ b/tests/modules/nf-core/mobsuite/recon/test.yml @@ -1,5 +1,5 @@ - name: mobsuite recon test_mobsuite_recon - command: nextflow run ./tests/modules/nf-core/mobsuite/recon -entry test_mobsuite_recon -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/mobsuite/recon -entry test_mobsuite_recon -c ./tests/config/nextflow.config tags: - mobsuite/recon - mobsuite diff --git a/tests/modules/nf-core/motus/downloaddb/test.yml b/tests/modules/nf-core/motus/downloaddb/test.yml index f059095f85e..5a85b5f3b76 100644 --- a/tests/modules/nf-core/motus/downloaddb/test.yml +++ b/tests/modules/nf-core/motus/downloaddb/test.yml @@ -1,5 +1,5 @@ - name: motus downloaddb test_motus_downloaddb - command: nextflow run ./tests/modules/nf-core/motus/downloaddb -entry test_motus_downloaddb -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/motus/downloaddb -entry test_motus_downloaddb -c ./tests/config/nextflow.config tags: - motus - motus/downloaddb diff --git a/tests/modules/nf-core/motus/profile/test.yml b/tests/modules/nf-core/motus/profile/test.yml index f63ad0f5ab2..fff6ad1dca5 100644 --- a/tests/modules/nf-core/motus/profile/test.yml +++ b/tests/modules/nf-core/motus/profile/test.yml @@ -1,5 +1,5 @@ - name: motus profile test_motus_profile_single_end - command: nextflow run ./tests/modules/nf-core/motus/profile -entry test_motus_profile_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/motus/profile -entry test_motus_profile_single_end -c ./tests/config/nextflow.config tags: - motus - motus/profile diff --git a/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml b/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml index 0ebbaa6643e..ca92fc798eb 100644 --- a/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml +++ b/tests/modules/nf-core/msisensorpro/msi_somatic/test.yml @@ -1,5 +1,5 @@ - name: msisensorpro msi_somatic test_msisensorpro_msi - command: nextflow run ./tests/modules/nf-core/msisensorpro/msi_somatic -entry test_msisensorpro_msi -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/msisensorpro/msi_somatic -entry test_msisensorpro_msi -c ./tests/config/nextflow.config tags: - msisensorpro/msi_somatic - msisensorpro diff --git a/tests/modules/nf-core/msisensorpro/scan/test.yml b/tests/modules/nf-core/msisensorpro/scan/test.yml index 91d7eae4819..d86d022fce5 100644 --- a/tests/modules/nf-core/msisensorpro/scan/test.yml +++ b/tests/modules/nf-core/msisensorpro/scan/test.yml @@ -1,5 +1,5 @@ - name: msisensorpro scan test_msisensorpro_scan - command: nextflow run ./tests/modules/nf-core/msisensorpro/scan -entry test_msisensorpro_scan -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/msisensorpro/scan -entry test_msisensorpro_scan -c ./tests/config/nextflow.config tags: - msisensorpro - msisensorpro/scan diff --git a/tests/modules/nf-core/ngscheckmate/ncm/test.yml b/tests/modules/nf-core/ngscheckmate/ncm/test.yml index ae550e4a29c..0d690400285 100644 --- a/tests/modules/nf-core/ngscheckmate/ncm/test.yml +++ b/tests/modules/nf-core/ngscheckmate/ncm/test.yml @@ -1,5 +1,5 @@ - name: ngscheckmate ncm test_ngscheckmate_ncm_bam - command: nextflow run ./tests/modules/nf-core/ngscheckmate/ncm -entry test_ngscheckmate_ncm_bam -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ngscheckmate/ncm -entry test_ngscheckmate_ncm_bam -c ./tests/config/nextflow.config tags: - ngscheckmate/ncm - ngscheckmate @@ -14,7 +14,7 @@ md5sum: fbb2bebd65b4f4e1e93c6bf5c08a6829 - name: ngscheckmate ncm test_ngscheckmate_ncm_vcf - command: nextflow run ./tests/modules/nf-core/ngscheckmate/ncm -entry test_ngscheckmate_ncm_vcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ngscheckmate/ncm -entry test_ngscheckmate_ncm_vcf -c ./tests/config/nextflow.config tags: - ngscheckmate/ncm - ngscheckmate diff --git a/tests/modules/nf-core/panaroo/run/test.yml b/tests/modules/nf-core/panaroo/run/test.yml index 249516bd184..7c198c68846 100644 --- a/tests/modules/nf-core/panaroo/run/test.yml +++ b/tests/modules/nf-core/panaroo/run/test.yml @@ -1,5 +1,5 @@ - name: panaroo run test_panaroo_run - command: nextflow run ./tests/modules/nf-core/panaroo/run -entry test_panaroo_run -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/panaroo/run -entry test_panaroo_run -c ./tests/config/nextflow.config tags: - panaroo/run - panaroo diff --git a/tests/modules/nf-core/phantompeakqualtools/test.yml b/tests/modules/nf-core/phantompeakqualtools/test.yml index 3d594758a89..8138cd0adc5 100644 --- a/tests/modules/nf-core/phantompeakqualtools/test.yml +++ b/tests/modules/nf-core/phantompeakqualtools/test.yml @@ -1,5 +1,5 @@ - name: phantompeakqualtools test_phantompeakqualtools_single_end - command: nextflow run ./tests/modules/nf-core/phantompeakqualtools -entry test_phantompeakqualtools_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/phantompeakqualtools -entry test_phantompeakqualtools_single_end -c ./tests/config/nextflow.config tags: - phantompeakqualtools files: @@ -11,7 +11,7 @@ md5sum: 6c2ede1aac4c574e3c72fbe09f15c03f - name: phantompeakqualtools test_phantompeakqualtools_paired_end - command: nextflow run ./tests/modules/nf-core/phantompeakqualtools -entry test_phantompeakqualtools_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/phantompeakqualtools -entry test_phantompeakqualtools_paired_end -c ./tests/config/nextflow.config tags: - phantompeakqualtools files: diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml b/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml index 11be38ddc02..26335c4f6f1 100644 --- a/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml +++ b/tests/modules/nf-core/picard/addorreplacereadgroups/test.yml @@ -1,5 +1,5 @@ - name: picard addorreplacereadgroups test_picard_addorreplacereadgroups - command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c ./tests/config/nextflow.config tags: - picard - picard/addorreplacereadgroups @@ -8,7 +8,7 @@ md5sum: 7b82f3461c2d80fc6a10385e78c9427f - path: output/picard/versions.yml - name: picard addorreplacereadgroups test_picard_addorreplacereadgroups stub - command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c tests/config/nextflow.config -stub + command: nextflow run ./tests/modules/nf-core/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c ./tests/config/nextflow.config -stub tags: - picard - picard/addorreplacereadgroups diff --git a/tests/modules/nf-core/picard/cleansam/test.yml b/tests/modules/nf-core/picard/cleansam/test.yml index 4ad571b5b89..9c05391e984 100644 --- a/tests/modules/nf-core/picard/cleansam/test.yml +++ b/tests/modules/nf-core/picard/cleansam/test.yml @@ -1,5 +1,5 @@ - name: picard cleansam test_picard_cleansam - command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c ./tests/config/nextflow.config tags: - picard/cleansam - picard diff --git a/tests/modules/nf-core/picard/createsequencedictionary/test.yml b/tests/modules/nf-core/picard/createsequencedictionary/test.yml index bc4e2f8bd23..ba2f1248264 100644 --- a/tests/modules/nf-core/picard/createsequencedictionary/test.yml +++ b/tests/modules/nf-core/picard/createsequencedictionary/test.yml @@ -1,5 +1,5 @@ - name: picard createsequencedictionary test_picard_createsequencedictionary - command: nextflow run ./tests/modules/nf-core/picard/createsequencedictionary -entry test_picard_createsequencedictionary -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/picard/createsequencedictionary -entry test_picard_createsequencedictionary -c ./tests/config/nextflow.config tags: - picard/createsequencedictionary - picard diff --git a/tests/modules/nf-core/picard/fixmateinformation/test.yml b/tests/modules/nf-core/picard/fixmateinformation/test.yml index 7b76007ae33..27de7cf3966 100644 --- a/tests/modules/nf-core/picard/fixmateinformation/test.yml +++ b/tests/modules/nf-core/picard/fixmateinformation/test.yml @@ -1,5 +1,5 @@ - name: picard fixmateinformation test_picard_fixmateinformation - command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c ./tests/config/nextflow.config tags: - picard - picard/fixmateinformation diff --git a/tests/modules/nf-core/picard/liftovervcf/test.yml b/tests/modules/nf-core/picard/liftovervcf/test.yml index ece723fb6ca..09bd2dd14c2 100644 --- a/tests/modules/nf-core/picard/liftovervcf/test.yml +++ b/tests/modules/nf-core/picard/liftovervcf/test.yml @@ -1,5 +1,5 @@ - name: picard liftovervcf test_picard_liftovervcf - command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf -c ./tests/config/nextflow.config tags: - picard/liftovervcf - picard @@ -11,7 +11,7 @@ - path: output/picard/versions.yml - name: picard liftovervcf test_picard_liftovervcf_stubs - command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c ./tests/config/nextflow.config -stub-run tags: - picard/liftovervcf - picard diff --git a/tests/modules/nf-core/plink2/extract/test.yml b/tests/modules/nf-core/plink2/extract/test.yml index 774423c5e72..457a31112b3 100644 --- a/tests/modules/nf-core/plink2/extract/test.yml +++ b/tests/modules/nf-core/plink2/extract/test.yml @@ -1,5 +1,5 @@ - name: plink2 extract test_plink2_extract - command: nextflow run ./tests/modules/nf-core/plink2/extract -entry test_plink2_extract -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/plink2/extract -entry test_plink2_extract -c ./tests/config/nextflow.config tags: - plink2/extract - plink2 diff --git a/tests/modules/nf-core/plink2/score/test.yml b/tests/modules/nf-core/plink2/score/test.yml index 17ea413a1c7..78f8a5354f2 100644 --- a/tests/modules/nf-core/plink2/score/test.yml +++ b/tests/modules/nf-core/plink2/score/test.yml @@ -1,5 +1,5 @@ - name: plink2 score test_plink2_score - command: nextflow run ./tests/modules/nf-core/plink2/score -entry test_plink2_score -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/plink2/score -entry test_plink2_score -c ./tests/config/nextflow.config tags: - plink2 - plink2/score diff --git a/tests/modules/nf-core/plink2/vcf/test.yml b/tests/modules/nf-core/plink2/vcf/test.yml index 7119c7c25d1..59a1e852f00 100644 --- a/tests/modules/nf-core/plink2/vcf/test.yml +++ b/tests/modules/nf-core/plink2/vcf/test.yml @@ -1,5 +1,5 @@ - name: plink2 vcf test_plink2_vcf - command: nextflow run ./tests/modules/nf-core/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config tags: - plink2 - plink2/vcf diff --git a/tests/modules/nf-core/prinseqplusplus/test.yml b/tests/modules/nf-core/prinseqplusplus/test.yml index 981f8431cd3..4b125043712 100644 --- a/tests/modules/nf-core/prinseqplusplus/test.yml +++ b/tests/modules/nf-core/prinseqplusplus/test.yml @@ -1,5 +1,5 @@ - name: prinseqplusplus test_prinseqplusplus_single_end - command: nextflow run ./tests/modules/nf-core/prinseqplusplus -entry test_prinseqplusplus_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/prinseqplusplus -entry test_prinseqplusplus_single_end -c ./tests/config/nextflow.config tags: - prinseqplusplus files: @@ -11,7 +11,7 @@ - path: output/prinseqplusplus/versions.yml - name: prinseqplusplus test_prinseqplusplus_paired_end - command: nextflow run ./tests/modules/nf-core/prinseqplusplus -entry test_prinseqplusplus_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/prinseqplusplus -entry test_prinseqplusplus_paired_end -c ./tests/config/nextflow.config tags: - prinseqplusplus files: diff --git a/tests/modules/nf-core/qualimap/bamqccram/test.yml b/tests/modules/nf-core/qualimap/bamqccram/test.yml index 7700ee5da0e..7b9a6495aa3 100644 --- a/tests/modules/nf-core/qualimap/bamqccram/test.yml +++ b/tests/modules/nf-core/qualimap/bamqccram/test.yml @@ -1,5 +1,5 @@ - name: qualimap bamqccram test_qualimap_bamqc - command: nextflow run ./tests/modules/nf-core/qualimap/bamqccram -entry test_qualimap_bamqc -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/qualimap/bamqccram -entry test_qualimap_bamqc -c ./tests/config/nextflow.config tags: - qualimap/bamqccram - qualimap diff --git a/tests/modules/nf-core/rtgtools/vcfeval/test.yml b/tests/modules/nf-core/rtgtools/vcfeval/test.yml index aa104b2558b..6fcbd2c25cf 100644 --- a/tests/modules/nf-core/rtgtools/vcfeval/test.yml +++ b/tests/modules/nf-core/rtgtools/vcfeval/test.yml @@ -1,5 +1,5 @@ - name: rtgtools vcfeval test_rtgtools_vcfeval - command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c ./tests/config/nextflow.config tags: - rtgtools - rtgtools/vcfeval @@ -37,7 +37,7 @@ md5sum: 270ed7a5a8e347b251eb4aa2198f98e8 - name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs - command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c ./tests/config/nextflow.config tags: - rtgtools - rtgtools/vcfeval diff --git a/tests/modules/nf-core/samtools/bam2fq/test.yml b/tests/modules/nf-core/samtools/bam2fq/test.yml index b72d47a861a..ab06fd3c8ca 100644 --- a/tests/modules/nf-core/samtools/bam2fq/test.yml +++ b/tests/modules/nf-core/samtools/bam2fq/test.yml @@ -1,5 +1,5 @@ - name: samtools bam2fq test_samtools_bam2fq_nosplit - command: nextflow run ./tests/modules/nf-core/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c ./tests/config/nextflow.config tags: - samtools/bam2fq - samtools @@ -9,7 +9,7 @@ md5sum: 4973eac1b6a8f090d5fcd4456d65a894 - name: samtools bam2fq test_samtools_bam2fq_withsplit - command: nextflow run ./tests/modules/nf-core/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c ./tests/config/nextflow.config tags: - samtools/bam2fq - samtools diff --git a/tests/modules/nf-core/samtools/convert/test.yml b/tests/modules/nf-core/samtools/convert/test.yml index 6e53abb1c20..aa0750b5670 100644 --- a/tests/modules/nf-core/samtools/convert/test.yml +++ b/tests/modules/nf-core/samtools/convert/test.yml @@ -1,5 +1,5 @@ - name: samtools convert test_samtools_convert_bamtocram - command: nextflow run ./tests/modules/nf-core/samtools/convert -entry test_samtools_convert_bamtocram -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/convert -entry test_samtools_convert_bamtocram -c ./tests/config/nextflow.config tags: - samtools - samtools/convert @@ -9,7 +9,7 @@ - path: output/samtools/versions.yml - name: samtools convert test_samtools_convert_cramtobam - command: nextflow run ./tests/modules/nf-core/samtools/convert -entry test_samtools_convert_cramtobam -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/convert -entry test_samtools_convert_cramtobam -c ./tests/config/nextflow.config tags: - samtools - samtools/convert diff --git a/tests/modules/nf-core/samtools/dict/test.yml b/tests/modules/nf-core/samtools/dict/test.yml index e75229a2209..388b2bc0216 100644 --- a/tests/modules/nf-core/samtools/dict/test.yml +++ b/tests/modules/nf-core/samtools/dict/test.yml @@ -1,5 +1,5 @@ - name: samtools dict test_samtools_dict - command: nextflow run ./tests/modules/nf-core/samtools/dict -entry test_samtools_dict -c tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/dict/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/dict -entry test_samtools_dict -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/dict/nextflow.config tags: - samtools - samtools/dict diff --git a/tests/modules/nf-core/samtools/faidx/test.yml b/tests/modules/nf-core/samtools/faidx/test.yml index e994e6a5a8e..7ad833de740 100644 --- a/tests/modules/nf-core/samtools/faidx/test.yml +++ b/tests/modules/nf-core/samtools/faidx/test.yml @@ -1,5 +1,5 @@ - name: samtools faidx test_samtools_faidx - command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx -c ./tests/config/nextflow.config tags: - samtools - samtools/faidx @@ -8,7 +8,7 @@ md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5 - path: output/samtools/versions.yml - name: samtools faidx test_samtools_faidx_bgzip - command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_bgzip -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_bgzip -c ./tests/config/nextflow.config tags: - samtools - samtools/faidx diff --git a/tests/modules/nf-core/samtools/mpileup/test.yml b/tests/modules/nf-core/samtools/mpileup/test.yml index 68acaadbd02..72a96def52d 100644 --- a/tests/modules/nf-core/samtools/mpileup/test.yml +++ b/tests/modules/nf-core/samtools/mpileup/test.yml @@ -1,5 +1,5 @@ - name: samtools mpileup test_samtools_mpileup - command: nextflow run ./tests/modules/nf-core/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/mpileup -entry test_samtools_mpileup -c ./tests/config/nextflow.config tags: - samtools - samtools/mpileup @@ -9,7 +9,7 @@ - path: output/samtools/versions.yml - name: samtools mpileup test_samtools_mpileup_intervals - command: nextflow run ./tests/modules/nf-core/samtools/mpileup -entry test_samtools_mpileup_intervals -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/mpileup -entry test_samtools_mpileup_intervals -c ./tests/config/nextflow.config tags: - samtools - samtools/mpileup diff --git a/tests/modules/nf-core/seqkit/pair/test.yml b/tests/modules/nf-core/seqkit/pair/test.yml index 23a96ab5f25..b27ed5443bc 100644 --- a/tests/modules/nf-core/seqkit/pair/test.yml +++ b/tests/modules/nf-core/seqkit/pair/test.yml @@ -1,5 +1,5 @@ - name: seqkit pair test_seqkit_pair - command: nextflow run ./tests/modules/nf-core/seqkit/pair -entry test_seqkit_pair -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/pair -entry test_seqkit_pair -c ./tests/config/nextflow.config tags: - seqkit/pair - seqkit diff --git a/tests/modules/nf-core/seqkit/replace/test.yml b/tests/modules/nf-core/seqkit/replace/test.yml index 178ea588eba..a83b809b2f8 100644 --- a/tests/modules/nf-core/seqkit/replace/test.yml +++ b/tests/modules/nf-core/seqkit/replace/test.yml @@ -1,5 +1,5 @@ - name: seqkit replace test_seqkit_replace - command: nextflow run ./tests/modules/nf-core/seqkit/replace -entry test_seqkit_replace -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/replace -entry test_seqkit_replace -c ./tests/config/nextflow.config tags: - seqkit - seqkit/replace @@ -10,7 +10,7 @@ md5sum: dc9d18b7836c9db00a3032fd191bd831 - name: seqkit replace test_seqkit_replace_uncomp - command: nextflow run ./tests/modules/nf-core/seqkit/replace -entry test_seqkit_replace_uncomp -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/replace -entry test_seqkit_replace_uncomp -c ./tests/config/nextflow.config tags: - seqkit - seqkit/replace diff --git a/tests/modules/nf-core/seqkit/split2/test.yml b/tests/modules/nf-core/seqkit/split2/test.yml index 20cdc152207..4bea4419b97 100644 --- a/tests/modules/nf-core/seqkit/split2/test.yml +++ b/tests/modules/nf-core/seqkit/split2/test.yml @@ -1,5 +1,5 @@ - name: seqkit split2 test_seqkit_split2_single_end_length - command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_length -c ./tests/config/nextflow.config tags: - seqkit - seqkit/split2 @@ -12,7 +12,7 @@ md5sum: 2d5a709d129be364687cc0b561efa532 - name: seqkit split2 test_seqkit_split2_single_end_size - command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_size -c ./tests/config/nextflow.config tags: - seqkit - seqkit/split2 @@ -25,7 +25,7 @@ md5sum: 490d00accd1092a8eca4e83ed809bad3 - name: seqkit split2 test_seqkit_split2_single_end_part - command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_single_end_part -c ./tests/config/nextflow.config tags: - seqkit - seqkit/split2 @@ -40,7 +40,7 @@ md5sum: 90431cd3d28954f656988230d4481115 - name: seqkit split2 test_seqkit_split2_paired_end_length - command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c ./tests/config/nextflow.config tags: - seqkit - seqkit/split2 @@ -57,7 +57,7 @@ md5sum: 9272afc1a126ae997a712edeef317f22 - name: seqkit split2 test_seqkit_split2_paired_end_size - command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c ./tests/config/nextflow.config tags: - seqkit - seqkit/split2 @@ -74,7 +74,7 @@ md5sum: af66912ae8abc493f77f70e3bf473144 - name: seqkit split2 test_seqkit_split2_paired_end_part - command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c ./tests/config/nextflow.config tags: - seqkit - seqkit/split2 diff --git a/tests/modules/nf-core/seqkit/stats/test.yml b/tests/modules/nf-core/seqkit/stats/test.yml index 3cd93ca3e64..bf7b7b2331d 100644 --- a/tests/modules/nf-core/seqkit/stats/test.yml +++ b/tests/modules/nf-core/seqkit/stats/test.yml @@ -1,5 +1,5 @@ - name: seqkit stats test_seqkit_stats_single_end - command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_single_end -c ./tests/config/nextflow.config tags: - seqkit/stats - seqkit @@ -10,7 +10,7 @@ md5sum: d67f0c16feb9df77b11f6c91bbdf9926 - name: seqkit stats test_seqkit_stats_paired_end - command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_paired_end -c ./tests/config/nextflow.config tags: - seqkit/stats - seqkit @@ -21,7 +21,7 @@ md5sum: bd8881933b953d07f2600e2e6a88ebf3 - name: seqkit stats test_seqkit_stats_nanopore - command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_nanopore -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_nanopore -c ./tests/config/nextflow.config tags: - seqkit/stats - seqkit @@ -32,7 +32,7 @@ md5sum: 565632701fbe048f7ba99f1865bd48ca - name: seqkit stats test_seqkit_stats_genome_fasta - command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_genome_fasta -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_genome_fasta -c ./tests/config/nextflow.config tags: - seqkit/stats - seqkit @@ -43,7 +43,7 @@ md5sum: 782fcdeaa922c8bb532ffa5808849d87 - name: seqkit stats test_seqkit_stats_transcriptome_fasta - command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c ./tests/config/nextflow.config tags: - seqkit/stats - seqkit diff --git a/tests/modules/nf-core/seqtk/rename/test.yml b/tests/modules/nf-core/seqtk/rename/test.yml index 60515500b5f..4409a899000 100644 --- a/tests/modules/nf-core/seqtk/rename/test.yml +++ b/tests/modules/nf-core/seqtk/rename/test.yml @@ -1,5 +1,5 @@ - name: seqtk rename test_seqtk_rename - command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename -c ./tests/config/nextflow.config tags: - seqtk - seqtk/rename @@ -9,7 +9,7 @@ - ">test1" - name: seqtk rename test_seqtk_rename_fq - command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename_fq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/rename -entry test_seqtk_rename_fq -c ./tests/config/nextflow.config tags: - seqtk - seqtk/rename diff --git a/tests/modules/nf-core/seqtk/seq/test.yml b/tests/modules/nf-core/seqtk/seq/test.yml index 1d0e3286232..ab1806daa1d 100644 --- a/tests/modules/nf-core/seqtk/seq/test.yml +++ b/tests/modules/nf-core/seqtk/seq/test.yml @@ -1,5 +1,5 @@ - name: seqtk seq test_seqtk_seq - command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq -c ./tests/config/nextflow.config tags: - seqtk/seq - seqtk @@ -8,7 +8,7 @@ md5sum: 50d73992c8c7e56dc095ef47ec52a754 - name: seqtk seq test_seqtk_seq_fq - command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq_fq -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/seqtk/seq -entry test_seqtk_seq_fq -c ./tests/config/nextflow.config tags: - seqtk/seq - seqtk diff --git a/tests/modules/nf-core/sexdeterrmine/test.yml b/tests/modules/nf-core/sexdeterrmine/test.yml index 73b98aed524..7dd2542d12f 100644 --- a/tests/modules/nf-core/sexdeterrmine/test.yml +++ b/tests/modules/nf-core/sexdeterrmine/test.yml @@ -1,5 +1,5 @@ - name: sexdeterrmine test_sexdeterrmine - command: nextflow run ./tests/modules/nf-core/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/sexdeterrmine -entry test_sexdeterrmine -c ./tests/config/nextflow.config tags: - sexdeterrmine files: diff --git a/tests/modules/nf-core/shasum/test.yml b/tests/modules/nf-core/shasum/test.yml index eab267eabcd..063844d0edd 100644 --- a/tests/modules/nf-core/shasum/test.yml +++ b/tests/modules/nf-core/shasum/test.yml @@ -1,5 +1,5 @@ - name: shasum test_shasum - command: nextflow run ./tests/modules/nf-core/shasum -entry test_shasum -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/shasum -entry test_shasum -c ./tests/config/nextflow.config tags: - shasum files: diff --git a/tests/modules/nf-core/shigatyper/test.yml b/tests/modules/nf-core/shigatyper/test.yml index 8b6ea1a0e2e..407a7906427 100644 --- a/tests/modules/nf-core/shigatyper/test.yml +++ b/tests/modules/nf-core/shigatyper/test.yml @@ -1,5 +1,5 @@ - name: shigatyper test_shigatyper_pe - command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_pe -c tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_pe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config tags: - shigatyper files: @@ -9,7 +9,7 @@ md5sum: d8ca45ed88dfba9bc570c01e4b49773b - name: shigatyper test_shigatyper_se - command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_se -c tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_se -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config tags: - shigatyper files: @@ -19,7 +19,7 @@ md5sum: 8bbf165da5a5df3b7771a33aad197eec - name: shigatyper test_shigatyper_ont - command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_ont -c tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config + command: nextflow run ./tests/modules/nf-core/shigatyper -entry test_shigatyper_ont -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shigatyper/nextflow.config tags: - shigatyper files: diff --git a/tests/modules/nf-core/sistr/test.yml b/tests/modules/nf-core/sistr/test.yml index 2012d84ea18..5ec8ac00f26 100644 --- a/tests/modules/nf-core/sistr/test.yml +++ b/tests/modules/nf-core/sistr/test.yml @@ -1,5 +1,5 @@ - name: sistr test_sistr - command: nextflow run ./tests/modules/nf-core/sistr -entry test_sistr -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/sistr -entry test_sistr -c ./tests/config/nextflow.config tags: - sistr files: diff --git a/tests/modules/nf-core/slimfastq/test.yml b/tests/modules/nf-core/slimfastq/test.yml index c008ec2219e..6010f2c6ce0 100644 --- a/tests/modules/nf-core/slimfastq/test.yml +++ b/tests/modules/nf-core/slimfastq/test.yml @@ -1,5 +1,5 @@ - name: slimfastq test_slimfastq_single_end - command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_single_end -c ./tests/config/nextflow.config tags: - slimfastq files: @@ -9,7 +9,7 @@ md5sum: f52351f5c9e6259af02745c8eae5c780 - name: slimfastq test_slimfastq_paired_end - command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_paired_end -c ./tests/config/nextflow.config tags: - slimfastq files: @@ -21,7 +21,7 @@ md5sum: 6239853705877651a4851c4cb6d62da4 - name: slimfastq test_slimfastq_nanopore - command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_nanopore -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_nanopore -c ./tests/config/nextflow.config tags: - slimfastq files: @@ -31,7 +31,7 @@ md5sum: 33153f1103482a2bd35cb2f4c337c5e8 - name: slimfastq test_slimfastq_pacbio - command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_pacbio -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/slimfastq -entry test_slimfastq_pacbio -c ./tests/config/nextflow.config tags: - slimfastq files: diff --git a/tests/modules/nf-core/snapaligner/index/test.yml b/tests/modules/nf-core/snapaligner/index/test.yml index bdb6871f31c..43898e069c8 100644 --- a/tests/modules/nf-core/snapaligner/index/test.yml +++ b/tests/modules/nf-core/snapaligner/index/test.yml @@ -1,5 +1,5 @@ - name: snapaligner index test_snapaligner_index - command: nextflow run ./tests/modules/nf-core/snapaligner/index -entry test_snapaligner_index -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snapaligner/index -entry test_snapaligner_index -c ./tests/config/nextflow.config tags: - snapaligner/index - snapaligner diff --git a/tests/modules/nf-core/snippy/run/test.yml b/tests/modules/nf-core/snippy/run/test.yml index 2bca969affb..dcdf41b84e0 100644 --- a/tests/modules/nf-core/snippy/run/test.yml +++ b/tests/modules/nf-core/snippy/run/test.yml @@ -1,6 +1,6 @@ - name: snippy run test_snippy_run command: | - nextflow run ./tests/modules/nf-core/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c ./tests/modules/nf-core/snippy/run/nextflow.config + nextflow run ./tests/modules/nf-core/snippy/run -entry test_snippy_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/snippy/run/nextflow.config tags: - snippy/run - snippy diff --git a/tests/modules/nf-core/snpsift/split/test.yml b/tests/modules/nf-core/snpsift/split/test.yml index 78e5cb99607..30fe340fd7b 100644 --- a/tests/modules/nf-core/snpsift/split/test.yml +++ b/tests/modules/nf-core/snpsift/split/test.yml @@ -1,5 +1,5 @@ - name: snpsift split test_snpsift_split_base - command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_base -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_base -c ./tests/config/nextflow.config tags: - snpsift/split - snpsift @@ -10,7 +10,7 @@ md5sum: 2b9f6b788db6c4fcbf258db763d8fab7 - name: snpsift split test_snpsift_split_gz - command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_gz -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_split_gz -c ./tests/config/nextflow.config tags: - snpsift/split - snpsift @@ -21,7 +21,7 @@ md5sum: 6bd63376670d6c1445caea2f31a3f579 - name: snpsift split test_snpsift_join - command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_join -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/snpsift/split -entry test_snpsift_join -c ./tests/config/nextflow.config tags: - snpsift/split - snpsift diff --git a/tests/modules/nf-core/sourmash/sketch/test.yml b/tests/modules/nf-core/sourmash/sketch/test.yml index be113397987..2497236b645 100644 --- a/tests/modules/nf-core/sourmash/sketch/test.yml +++ b/tests/modules/nf-core/sourmash/sketch/test.yml @@ -1,5 +1,5 @@ - name: sourmash sketch test_sourmash_sketch - command: nextflow run ./tests/modules/nf-core/sourmash/sketch -entry test_sourmash_sketch -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/sourmash/sketch -entry test_sourmash_sketch -c ./tests/config/nextflow.config tags: - sourmash - sourmash/sketch diff --git a/tests/modules/nf-core/srst2/srst2/main.nf b/tests/modules/nf-core/srst2/srst2/main.nf index aaeed0178c8..27eb58a7f0f 100644 --- a/tests/modules/nf-core/srst2/srst2/main.nf +++ b/tests/modules/nf-core/srst2/srst2/main.nf @@ -35,7 +35,7 @@ workflow test_srst2_srst2_paired_end { [ id:'test', single_end:false, db:"gene"], // meta map [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ], - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] SRST2_SRST2(input) @@ -46,7 +46,7 @@ workflow test_srst2_srst2_single_end { input = [ [ id:'test', single_end:true, db:"gene" ], // meta map file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config ] SRST2_SRST2(input) diff --git a/tests/modules/nf-core/srst2/srst2/test.yml b/tests/modules/nf-core/srst2/srst2/test.yml index 6d70b5b4e7b..7d8a6cba546 100644 --- a/tests/modules/nf-core/srst2/srst2/test.yml +++ b/tests/modules/nf-core/srst2/srst2/test.yml @@ -1,12 +1,12 @@ - name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db - command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_exit -c ./tests/config/nextflow.config tags: - srst2/srst2 - srst2 exit_code: 1 - name: srst2 srst2 test_srst2_srst2_mlst - command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_mlst -c ./tests/config/nextflow.config tags: - srst2/srst2 - srst2 @@ -21,7 +21,7 @@ md5sum: a0c256a2fd3636069710b8ef22ee5ea7 - name: srst2 srst2 test_srst2_srst2_paired_end - command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_paired_end -c ./tests/config/nextflow.config tags: - srst2/srst2 - srst2 @@ -35,7 +35,7 @@ md5sum: b446a70f1a2b4f60757829bcd744a214 - name: srst2 srst2 test_srst2_srst2_single_end - command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/srst2/srst2 -entry test_srst2_srst2_single_end -c ./tests/config/nextflow.config tags: - srst2/srst2 - srst2 diff --git a/tests/modules/nf-core/ssuissero/test.yml b/tests/modules/nf-core/ssuissero/test.yml index a2aaf250e4c..4fa8af5d71a 100644 --- a/tests/modules/nf-core/ssuissero/test.yml +++ b/tests/modules/nf-core/ssuissero/test.yml @@ -1,5 +1,5 @@ - name: ssuissero test_ssuissero - command: nextflow run ./tests/modules/nf-core/ssuissero -entry test_ssuissero -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/ssuissero -entry test_ssuissero -c ./tests/config/nextflow.config tags: - ssuissero files: diff --git a/tests/modules/nf-core/stadeniolib/scramble/test.yml b/tests/modules/nf-core/stadeniolib/scramble/test.yml index e7064d946af..d208a67b769 100644 --- a/tests/modules/nf-core/stadeniolib/scramble/test.yml +++ b/tests/modules/nf-core/stadeniolib/scramble/test.yml @@ -1,5 +1,5 @@ - name: stadeniolib test_stadeniolib - command: nextflow run ./tests/modules/nf-core/stadeniolib -entry test_stadeniolib -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/stadeniolib -entry test_stadeniolib -c ./tests/config/nextflow.config tags: - stadeniolib files: diff --git a/tests/modules/nf-core/stranger/test.yml b/tests/modules/nf-core/stranger/test.yml index b68c867d009..6a8721cc6d6 100644 --- a/tests/modules/nf-core/stranger/test.yml +++ b/tests/modules/nf-core/stranger/test.yml @@ -1,5 +1,5 @@ - name: stranger test_stranger - command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger -c ./tests/config/nextflow.config tags: - stranger files: @@ -13,7 +13,7 @@ md5sum: 5ec35fd835fb1be50bc3e7c004310fc0 - name: stranger test_stranger_without_optional_variant_catalog - command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c ./tests/config/nextflow.config tags: - stranger files: @@ -27,7 +27,7 @@ md5sum: 8558542a007e90ea5dcdceed3f12585d - name: stranger test_stranger_without_optional_variant_catalog_stubs - command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run + command: nextflow run ./tests/modules/nf-core/stranger -entry test_stranger_without_optional_variant_catalog -c ./tests/config/nextflow.config -stub-run tags: - stranger files: diff --git a/tests/modules/nf-core/transdecoder/longorf/test.yml b/tests/modules/nf-core/transdecoder/longorf/test.yml index f45de1b502d..3a06da79103 100644 --- a/tests/modules/nf-core/transdecoder/longorf/test.yml +++ b/tests/modules/nf-core/transdecoder/longorf/test.yml @@ -1,5 +1,5 @@ - name: transdecoder longorf test_transdecoder_longorf - command: nextflow run ./tests/modules/nf-core/transdecoder/longorf -entry test_transdecoder_longorf -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/transdecoder/longorf -entry test_transdecoder_longorf -c ./tests/config/nextflow.config tags: - transdecoder - transdecoder/longorf diff --git a/tests/modules/nf-core/transdecoder/predict/test.yml b/tests/modules/nf-core/transdecoder/predict/test.yml index 88575684df3..31cf06b4987 100644 --- a/tests/modules/nf-core/transdecoder/predict/test.yml +++ b/tests/modules/nf-core/transdecoder/predict/test.yml @@ -1,5 +1,5 @@ - name: transdecoder predict test_transdecoder_predict - command: nextflow run ./tests/modules/nf-core/transdecoder/predict -entry test_transdecoder_predict -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/transdecoder/predict -entry test_transdecoder_predict -c ./tests/config/nextflow.config tags: - transdecoder - transdecoder/predict diff --git a/tests/modules/nf-core/umitools/extract/test.yml b/tests/modules/nf-core/umitools/extract/test.yml index 7f2b8a0a9b7..0355061afae 100644 --- a/tests/modules/nf-core/umitools/extract/test.yml +++ b/tests/modules/nf-core/umitools/extract/test.yml @@ -1,5 +1,5 @@ - name: umitools extract test_umitools_extract_single_end - command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_single_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_single_end -c ./tests/config/nextflow.config tags: - umitools/extract - umitools @@ -12,7 +12,7 @@ md5sum: 397e6972343f9d7b8eae387fc18c12c7 - name: umitools extract test_umitools_extract_paired_end - command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_paired_end -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/umitools/extract -entry test_umitools_extract_paired_end -c ./tests/config/nextflow.config tags: - umitools/extract - umitools diff --git a/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml b/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml index b730c5a12b0..3a2a51c5999 100644 --- a/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml +++ b/tests/modules/nf-core/vcflib/vcfbreakmulti/test.yml @@ -1,5 +1,5 @@ - name: vcflib vcfbreakmulti - command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config + command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c ./tests/config/nextflow.config tags: - vcflib/vcfbreakmulti - vcflib @@ -8,7 +8,7 @@ md5sum: 666d2d970399cf219dc1dc1eadff9170 - name: vcflib vcfbreakmulti stub - command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config -stub + command: nextflow run ./tests/modules/nf-core/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c ./tests/config/nextflow.config -stub tags: - vcflib/vcfbreakmulti - vcflib From c0866485ba6ac5da10ac4add8653d676b7964940 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 3 Oct 2022 21:03:34 +0100 Subject: [PATCH 8/9] Update relative paths in tests --- tests/modules/nf-core/abacas/main.nf | 2 +- tests/modules/nf-core/abricate/run/main.nf | 2 +- tests/modules/nf-core/abricate/summary/main.nf | 4 ++-- tests/modules/nf-core/adapterremoval/main.nf | 4 ++-- .../nf-core/adapterremovalfixprefix/main.nf | 4 ++-- tests/modules/nf-core/agrvate/main.nf | 2 +- tests/modules/nf-core/allelecounter/main.nf | 2 +- tests/modules/nf-core/ampir/main.nf | 2 +- tests/modules/nf-core/amplify/predict/main.nf | 4 ++-- tests/modules/nf-core/amps/main.nf | 12 ++++++------ .../modules/nf-core/amrfinderplus/run/main.nf | 4 ++-- .../nf-core/amrfinderplus/update/main.nf | 2 +- tests/modules/nf-core/angsd/docounts/main.nf | 2 +- .../nf-core/antismash/antismashlite/main.nf | 14 +++++++------- .../antismashlitedownloaddatabases/main.nf | 8 ++++---- tests/modules/nf-core/ariba/getref/main.nf | 2 +- tests/modules/nf-core/ariba/run/main.nf | 4 ++-- tests/modules/nf-core/arriba/main.nf | 6 +++--- tests/modules/nf-core/artic/guppyplex/main.nf | 2 +- tests/modules/nf-core/artic/minion/main.nf | 4 ++-- tests/modules/nf-core/ascat/main.nf | 14 +++++++------- tests/modules/nf-core/assemblyscan/main.nf | 2 +- tests/modules/nf-core/ataqv/ataqv/main.nf | 4 ++-- tests/modules/nf-core/ataqv/mkarv/main.nf | 4 ++-- tests/modules/nf-core/atlas/call/main.nf | 2 +- tests/modules/nf-core/atlas/pmd/main.nf | 2 +- tests/modules/nf-core/atlas/recal/main.nf | 2 +- tests/modules/nf-core/atlas/splitmerge/main.nf | 2 +- tests/modules/nf-core/bakta/main.nf | 2 +- tests/modules/nf-core/bamaligncleaner/main.nf | 2 +- tests/modules/nf-core/bamcmp/main.nf | 14 +++++++------- tests/modules/nf-core/bamtools/convert/main.nf | 18 +++++++++--------- tests/modules/nf-core/bamtools/split/main.nf | 4 ++-- tests/modules/nf-core/bamtools/stats/main.nf | 2 +- tests/modules/nf-core/bamutil/trimbam/main.nf | 2 +- tests/modules/nf-core/bandage/image/main.nf | 2 +- tests/modules/nf-core/bases2fastq/main.nf | 4 ++-- tests/modules/nf-core/bbmap/align/main.nf | 6 +++--- tests/modules/nf-core/bbmap/bbduk/main.nf | 2 +- tests/modules/nf-core/bbmap/bbsplit/main.nf | 4 ++-- tests/modules/nf-core/bbmap/clumpify/main.nf | 2 +- tests/modules/nf-core/bbmap/index/main.nf | 2 +- tests/modules/nf-core/bbmap/pileup/main.nf | 2 +- .../modules/nf-core/bcftools/annotate/main.nf | 2 +- tests/modules/nf-core/bcftools/concat/main.nf | 2 +- .../modules/nf-core/bcftools/consensus/main.nf | 2 +- tests/modules/nf-core/bcftools/convert/main.nf | 4 ++-- tests/modules/nf-core/bcftools/filter/main.nf | 2 +- tests/modules/nf-core/bcftools/index/main.nf | 4 ++-- tests/modules/nf-core/bcftools/isec/main.nf | 2 +- tests/modules/nf-core/bcftools/merge/main.nf | 6 +++--- tests/modules/nf-core/bcftools/mpileup/main.nf | 2 +- tests/modules/nf-core/bcftools/norm/main.nf | 2 +- tests/modules/nf-core/bcftools/query/main.nf | 2 +- .../modules/nf-core/bcftools/reheader/main.nf | 2 +- tests/modules/nf-core/bcftools/roh/main.nf | 2 +- tests/modules/nf-core/bcftools/sort/main.nf | 2 +- tests/modules/nf-core/bcftools/stats/main.nf | 2 +- tests/modules/nf-core/bcftools/view/main.nf | 2 +- tests/modules/nf-core/bcl2fastq/main.nf | 4 ++-- tests/modules/nf-core/bclconvert/main.nf | 4 ++-- .../modules/nf-core/bedtools/bamtobed/main.nf | 2 +- .../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 +- .../nf-core/bedtools/makewindows/main.nf | 2 +- .../modules/nf-core/bedtools/maskfasta/main.nf | 2 +- tests/modules/nf-core/bedtools/merge/main.nf | 2 +- tests/modules/nf-core/bedtools/slop/main.nf | 2 +- tests/modules/nf-core/bedtools/sort/main.nf | 2 +- tests/modules/nf-core/bedtools/split/main.nf | 2 +- .../modules/nf-core/bedtools/subtract/main.nf | 2 +- .../biobambam/bammarkduplicates2/main.nf | 2 +- .../modules/nf-core/biobambam/bammerge/main.nf | 2 +- .../nf-core/biobambam/bamsormadup/main.nf | 2 +- tests/modules/nf-core/biscuit/align/main.nf | 6 +++--- .../nf-core/biscuit/biscuitblaster/main.nf | 6 +++--- tests/modules/nf-core/biscuit/bsconv/main.nf | 4 ++-- tests/modules/nf-core/biscuit/epiread/main.nf | 4 ++-- tests/modules/nf-core/biscuit/index/main.nf | 2 +- tests/modules/nf-core/biscuit/mergecg/main.nf | 4 ++-- tests/modules/nf-core/biscuit/pileup/main.nf | 4 ++-- tests/modules/nf-core/biscuit/qc/main.nf | 4 ++-- tests/modules/nf-core/biscuit/vcf2bed/main.nf | 2 +- tests/modules/nf-core/bismark/align/main.nf | 6 +++--- .../nf-core/bismark/deduplicate/main.nf | 2 +- .../nf-core/bismark/genomepreparation/main.nf | 2 +- .../bismark/methylationextractor/main.nf | 4 ++-- tests/modules/nf-core/bismark/report/main.nf | 10 +++++----- tests/modules/nf-core/bismark/summary/main.nf | 10 +++++----- tests/modules/nf-core/blast/blastn/main.nf | 4 ++-- .../modules/nf-core/blast/makeblastdb/main.nf | 2 +- tests/modules/nf-core/blast/tblastn/main.nf | 4 ++-- tests/modules/nf-core/bowtie/align/main.nf | 4 ++-- .../modules/nf-core/bowtie/build_test/main.nf | 2 +- tests/modules/nf-core/bowtie2/align/main.nf | 4 ++-- .../modules/nf-core/bowtie2/build_test/main.nf | 2 +- tests/modules/nf-core/bracken/bracken/main.nf | 6 +++--- .../bracken/combinebrackenoutputs/main.nf | 8 ++++---- tests/modules/nf-core/busco/main.nf | 2 +- tests/modules/nf-core/bwa/aln/main.nf | 4 ++-- tests/modules/nf-core/bwa/index/main.nf | 2 +- tests/modules/nf-core/bwa/mem/main.nf | 4 ++-- tests/modules/nf-core/bwa/sampe/main.nf | 6 +++--- tests/modules/nf-core/bwa/samse/main.nf | 6 +++--- tests/modules/nf-core/bwamem2/index/main.nf | 2 +- tests/modules/nf-core/bwamem2/mem/main.nf | 4 ++-- tests/modules/nf-core/bwameth/align/main.nf | 4 ++-- tests/modules/nf-core/bwameth/index/main.nf | 2 +- tests/modules/nf-core/cat/cat/main.nf | 6 +++--- tests/modules/nf-core/cat/fastq/main.nf | 2 +- tests/modules/nf-core/cellranger/count/main.nf | 6 +++--- .../modules/nf-core/cellranger/mkfastq/main.nf | 4 ++-- tests/modules/nf-core/cellranger/mkgtf/main.nf | 2 +- tests/modules/nf-core/cellranger/mkref/main.nf | 2 +- .../nf-core/centrifuge/centrifuge/main.nf | 4 ++-- .../modules/nf-core/centrifuge/kreport/main.nf | 6 +++--- tests/modules/nf-core/checkm/lineagewf/main.nf | 2 +- tests/modules/nf-core/checkm/qa/main.nf | 8 ++++---- tests/modules/nf-core/chromap/chromap/main.nf | 6 +++--- tests/modules/nf-core/chromap/index/main.nf | 2 +- tests/modules/nf-core/clonalframeml/main.nf | 2 +- tests/modules/nf-core/cmseq/polymut/main.nf | 2 +- .../modules/nf-core/cnvkit/antitarget/main.nf | 2 +- tests/modules/nf-core/cnvkit/batch/main.nf | 8 ++++---- tests/modules/nf-core/cnvkit/reference/main.nf | 2 +- .../modules/nf-core/cnvpytor/callcnvs/main.nf | 2 +- .../modules/nf-core/cnvpytor/histogram/main.nf | 2 +- .../nf-core/cnvpytor/importreaddepth/main.nf | 2 +- .../modules/nf-core/cnvpytor/partition/main.nf | 2 +- tests/modules/nf-core/cnvpytor/view/main.nf | 2 +- .../controlfreec/assesssignificance/main.nf | 6 +++--- .../modules/nf-core/controlfreec/freec/main.nf | 4 ++-- .../nf-core/controlfreec/freec2bed/main.nf | 6 +++--- .../nf-core/controlfreec/freec2circos/main.nf | 6 +++--- .../nf-core/controlfreec/makegraph/main.nf | 6 +++--- tests/modules/nf-core/cooler/cload/main.nf | 12 ++++++------ tests/modules/nf-core/cooler/digest/main.nf | 2 +- tests/modules/nf-core/cooler/dump/main.nf | 2 +- tests/modules/nf-core/cooler/merge/main.nf | 4 ++-- tests/modules/nf-core/cooler/zoomify/main.nf | 2 +- tests/modules/nf-core/csvtk/concat/main.nf | 2 +- tests/modules/nf-core/csvtk/split/main.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +++--- .../nf-core/custom/getchromsizes/main.nf | 2 +- .../custom/sratoolsncbisettings/main.nf | 2 +- tests/modules/nf-core/cutadapt/main.nf | 2 +- tests/modules/nf-core/damageprofiler/main.nf | 2 +- tests/modules/nf-core/dastool/dastool/main.nf | 8 ++++---- .../nf-core/dastool/fastatocontig2bin/main.nf | 8 ++++---- .../nf-core/dastool/scaffolds2bin/main.nf | 8 ++++---- tests/modules/nf-core/dedup/main.nf | 2 +- .../nf-core/deeparg/downloaddata/main.nf | 2 +- tests/modules/nf-core/deeparg/predict/main.nf | 4 ++-- tests/modules/nf-core/deepbgc/download/main.nf | 2 +- tests/modules/nf-core/deepbgc/pipeline/main.nf | 8 ++++---- .../nf-core/deeptools/bamcoverage/main.nf | 2 +- .../nf-core/deeptools/computematrix/main.nf | 2 +- .../nf-core/deeptools/plotfingerprint/main.nf | 2 +- .../nf-core/deeptools/plotheatmap/main.nf | 2 +- .../nf-core/deeptools/plotprofile/main.nf | 2 +- tests/modules/nf-core/deepvariant/main.nf | 4 ++-- tests/modules/nf-core/delly/call/main.nf | 2 +- tests/modules/nf-core/diamond/blastp/main.nf | 4 ++-- tests/modules/nf-core/diamond/blastx/main.nf | 4 ++-- tests/modules/nf-core/diamond/makedb/main.nf | 2 +- tests/modules/nf-core/dragmap/align/main.nf | 4 ++-- .../modules/nf-core/dragmap/hashtable/main.nf | 2 +- tests/modules/nf-core/dragonflye/main.nf | 4 ++-- .../nf-core/dshbio/exportsegments/main.nf | 2 +- tests/modules/nf-core/dshbio/filterbed/main.nf | 2 +- .../modules/nf-core/dshbio/filtergff3/main.nf | 2 +- tests/modules/nf-core/dshbio/splitbed/main.nf | 2 +- tests/modules/nf-core/dshbio/splitgff3/main.nf | 2 +- tests/modules/nf-core/ectyper/main.nf | 2 +- tests/modules/nf-core/eido/convert/main.nf | 2 +- tests/modules/nf-core/eido/validate/main.nf | 2 +- tests/modules/nf-core/elprep/filter/main.nf | 2 +- tests/modules/nf-core/elprep/merge/main.nf | 4 ++-- tests/modules/nf-core/elprep/split/main.nf | 2 +- tests/modules/nf-core/emboss/seqret/main.nf | 4 ++-- tests/modules/nf-core/emmtyper/main.nf | 2 +- tests/modules/nf-core/endorspy/main.nf | 10 +++++----- tests/modules/nf-core/ensemblvep/main.nf | 12 ++++++------ .../nf-core/entrezdirect/esummary/main.nf | 2 +- .../nf-core/entrezdirect/xtract/main.nf | 4 ++-- tests/modules/nf-core/epang/main.nf | 2 +- tests/modules/nf-core/expansionhunter/main.nf | 2 +- tests/modules/nf-core/faqcs/main.nf | 2 +- tests/modules/nf-core/fargene/main.nf | 4 ++-- tests/modules/nf-core/fastani/main.nf | 2 +- tests/modules/nf-core/fastawindows/main.nf | 2 +- tests/modules/nf-core/fastk/fastk/main.nf | 2 +- tests/modules/nf-core/fastk/histex/main.nf | 4 ++-- tests/modules/nf-core/fastk/merge/main.nf | 4 ++-- tests/modules/nf-core/fastp/main.nf | 2 +- tests/modules/nf-core/fastqc/main.nf | 2 +- tests/modules/nf-core/fastqscan/main.nf | 2 +- tests/modules/nf-core/fasttree/main.nf | 2 +- tests/modules/nf-core/fcs/fcsadaptor/main.nf | 2 +- tests/modules/nf-core/ffq/main.nf | 2 +- .../fgbio/callmolecularconsensusreads/main.nf | 4 ++-- tests/modules/nf-core/fgbio/fastqtobam/main.nf | 2 +- .../nf-core/fgbio/groupreadsbyumi/main.nf | 2 +- tests/modules/nf-core/fgbio/sortbam/main.nf | 2 +- tests/modules/nf-core/filtlong/main.nf | 2 +- tests/modules/nf-core/flash/main.nf | 2 +- tests/modules/nf-core/flye/main.nf | 2 +- tests/modules/nf-core/fq/lint/main.nf | 2 +- tests/modules/nf-core/freebayes/main.nf | 2 +- tests/modules/nf-core/gamma/gamma/main.nf | 2 +- .../nf-core/gappa/examineassign/main.nf | 2 +- .../modules/nf-core/gappa/examinegraft/main.nf | 2 +- .../nf-core/gappa/examineheattree/main.nf | 2 +- .../nf-core/gatk/indelrealigner/main.nf | 4 ++-- .../gatk/realignertargetcreator/main.nf | 2 +- .../nf-core/gatk/unifiedgenotyper/main.nf | 2 +- tests/modules/nf-core/gatk4/applybqsr/main.nf | 2 +- .../nf-core/gatk4/applybqsrspark/main.nf | 2 +- tests/modules/nf-core/gatk4/applyvqsr/main.nf | 4 ++-- .../nf-core/gatk4/baserecalibrator/main.nf | 2 +- .../gatk4/baserecalibratorspark/main.nf | 2 +- .../nf-core/gatk4/bedtointervallist/main.nf | 2 +- .../gatk4/calculatecontamination/main.nf | 4 ++-- .../gatk4/calibratedragstrmodel/main.nf | 2 +- .../nf-core/gatk4/cnnscorevariants/main.nf | 2 +- .../nf-core/gatk4/collectreadcounts/main.nf | 2 +- .../nf-core/gatk4/collectsvevidence/main.nf | 2 +- .../modules/nf-core/gatk4/combinegvcfs/main.nf | 2 +- .../nf-core/gatk4/composestrtablefile/main.nf | 2 +- .../gatk4/createsequencedictionary/main.nf | 2 +- .../gatk4/createsomaticpanelofnormals/main.nf | 4 ++-- .../gatk4/estimatelibrarycomplexity/main.nf | 2 +- tests/modules/nf-core/gatk4/fastqtosam/main.nf | 2 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 2 +- .../gatk4/filtervarianttranches/main.nf | 6 +++--- .../nf-core/gatk4/gatherbqsrreports/main.nf | 2 +- .../gatk4/gatherpileupsummaries/main.nf | 2 +- .../nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- .../nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- .../nf-core/gatk4/getpileupsummaries/main.nf | 2 +- .../nf-core/gatk4/haplotypecaller/main.nf | 2 +- .../nf-core/gatk4/indexfeaturefile/main.nf | 2 +- .../nf-core/gatk4/intervallisttobed/main.nf | 2 +- .../nf-core/gatk4/intervallisttools/main.nf | 4 ++-- .../gatk4/learnreadorientationmodel/main.nf | 2 +- .../gatk4/leftalignandtrimvariants/main.nf | 2 +- .../nf-core/gatk4/markduplicates/main.nf | 4 ++-- .../nf-core/gatk4/markduplicatesspark/main.nf | 6 +++--- .../nf-core/gatk4/mergebamalignment/main.nf | 2 +- .../nf-core/gatk4/mergemutectstats/main.nf | 2 +- tests/modules/nf-core/gatk4/mergevcfs/main.nf | 2 +- tests/modules/nf-core/gatk4/mutect2/main.nf | 8 ++++---- .../nf-core/gatk4/printsvevidence/main.nf | 6 +++--- .../modules/nf-core/gatk4/reblockgvcf/main.nf | 2 +- tests/modules/nf-core/gatk4/revertsam/main.nf | 2 +- tests/modules/nf-core/gatk4/samtofastq/main.nf | 2 +- .../nf-core/gatk4/selectvariants/main.nf | 2 +- .../nf-core/gatk4/splitintervals/main.nf | 2 +- .../nf-core/gatk4/splitncigarreads/main.nf | 2 +- .../nf-core/gatk4/variantfiltration/main.nf | 2 +- .../nf-core/gatk4/variantrecalibrator/main.nf | 4 ++-- tests/modules/nf-core/gecco/run/main.nf | 2 +- tests/modules/nf-core/genescopefk/main.nf | 6 +++--- tests/modules/nf-core/genmap/index/main.nf | 2 +- .../modules/nf-core/genmap/mappability/main.nf | 4 ++-- tests/modules/nf-core/genmod/annotate/main.nf | 2 +- tests/modules/nf-core/genmod/compound/main.nf | 2 +- tests/modules/nf-core/genmod/models/main.nf | 2 +- tests/modules/nf-core/genmod/score/main.nf | 2 +- tests/modules/nf-core/genomescope2/main.nf | 6 +++--- tests/modules/nf-core/genotyphi/parse/main.nf | 4 ++-- tests/modules/nf-core/genrich/main.nf | 8 ++++---- tests/modules/nf-core/gfaffix/main.nf | 2 +- 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++-- .../nf-core/hamronization/summarize/main.nf | 6 +++--- tests/modules/nf-core/haplocheck/main.nf | 2 +- .../nf-core/haplogrep2/classify/main.nf | 2 +- tests/modules/nf-core/happy/happy/main.nf | 2 +- tests/modules/nf-core/happy/prepy/main.nf | 2 +- tests/modules/nf-core/hicap/main.nf | 2 +- tests/modules/nf-core/hifiasm/main.nf | 2 +- tests/modules/nf-core/hisat2/align/main.nf | 6 +++--- .../modules/nf-core/hisat2/build_test/main.nf | 4 ++-- .../nf-core/hisat2/extractsplicesites/main.nf | 2 +- .../modules/nf-core/hmmcopy/gccounter/main.nf | 2 +- .../nf-core/hmmcopy/generatemap/main.nf | 2 +- .../modules/nf-core/hmmcopy/mapcounter/main.nf | 4 ++-- .../nf-core/hmmcopy/readcounter/main.nf | 2 +- tests/modules/nf-core/hmmer/eslalimask/main.nf | 4 ++-- .../modules/nf-core/hmmer/eslreformat/main.nf | 8 ++++---- tests/modules/nf-core/hmmer/hmmalign/main.nf | 4 ++-- tests/modules/nf-core/hmmer/hmmbuild/main.nf | 2 +- tests/modules/nf-core/hmmer/hmmsearch/main.nf | 2 +- tests/modules/nf-core/hmtnote/main.nf | 2 +- .../nf-core/homer/annotatepeaks/main.nf | 2 +- tests/modules/nf-core/homer/findpeaks/main.nf | 4 ++-- .../nf-core/homer/maketagdirectory/main.nf | 2 +- .../modules/nf-core/homer/makeucscfile/main.nf | 4 ++-- tests/modules/nf-core/homer/pos2bed/main.nf | 6 +++--- tests/modules/nf-core/hpsuissero/main.nf | 2 +- .../modules/nf-core/ichorcna/createpon/main.nf | 2 +- tests/modules/nf-core/ichorcna/run/main.nf | 10 +++++----- tests/modules/nf-core/idr/main.nf | 2 +- .../modules/nf-core/imputeme/vcftoprs/main.nf | 2 +- tests/modules/nf-core/instrain/profile/main.nf | 2 +- tests/modules/nf-core/iqtree/main.nf | 2 +- tests/modules/nf-core/ismapper/main.nf | 2 +- tests/modules/nf-core/isoseq3/cluster/main.nf | 2 +- tests/modules/nf-core/isoseq3/refine/main.nf | 2 +- tests/modules/nf-core/ivar/consensus/main.nf | 2 +- tests/modules/nf-core/ivar/trim/main.nf | 2 +- tests/modules/nf-core/ivar/variants/main.nf | 2 +- tests/modules/nf-core/jupyternotebook/main.nf | 6 +++--- tests/modules/nf-core/kaiju/kaiju/main.nf | 4 ++-- .../modules/nf-core/kaiju/kaiju2krona/main.nf | 6 +++--- .../modules/nf-core/kaiju/kaiju2table/main.nf | 6 +++--- tests/modules/nf-core/kallisto/index/main.nf | 2 +- .../nf-core/kallistobustools/count/main.nf | 4 ++-- .../nf-core/kallistobustools/ref/main.nf | 2 +- tests/modules/nf-core/kat/hist/main.nf | 2 +- .../nf-core/khmer/normalizebymedian/main.nf | 6 +++--- .../modules/nf-core/khmer/uniquekmers/main.nf | 2 +- tests/modules/nf-core/kleborate/main.nf | 2 +- tests/modules/nf-core/kraken2/kraken2/main.nf | 4 ++-- .../krakentools/combinekreports/main.nf | 6 +++--- .../nf-core/krakentools/kreport2krona/main.nf | 6 +++--- tests/modules/nf-core/krona/kronadb/main.nf | 2 +- .../nf-core/krona/ktimporttaxonomy/main.nf | 4 ++-- .../modules/nf-core/krona/ktimporttext/main.nf | 2 +- .../nf-core/krona/ktupdatetaxonomy/main.nf | 2 +- tests/modules/nf-core/last/dotplot/main.nf | 2 +- tests/modules/nf-core/last/lastal/main.nf | 4 ++-- tests/modules/nf-core/last/lastdb/main.nf | 2 +- tests/modules/nf-core/last/mafconvert/main.nf | 2 +- tests/modules/nf-core/last/mafswap/main.nf | 2 +- tests/modules/nf-core/last/postmask/main.nf | 2 +- tests/modules/nf-core/last/split/main.nf | 2 +- tests/modules/nf-core/last/train/main.nf | 4 ++-- tests/modules/nf-core/leehom/main.nf | 4 ++-- tests/modules/nf-core/legsta/main.nf | 2 +- tests/modules/nf-core/lima/main.nf | 2 +- tests/modules/nf-core/lissero/main.nf | 2 +- tests/modules/nf-core/lofreq/call/main.nf | 2 +- .../nf-core/lofreq/callparallel/main.nf | 2 +- tests/modules/nf-core/lofreq/filter/main.nf | 2 +- tests/modules/nf-core/lofreq/indelqual/main.nf | 2 +- tests/modules/nf-core/macrel/contigs/main.nf | 2 +- tests/modules/nf-core/macs2/callpeak/main.nf | 6 +++--- tests/modules/nf-core/mafft/main.nf | 2 +- tests/modules/nf-core/malt/build_test/main.nf | 4 ++-- tests/modules/nf-core/malt/run/main.nf | 6 +++--- tests/modules/nf-core/maltextract/main.nf | 10 +++++----- .../nf-core/manta/convertinversion/main.nf | 4 ++-- tests/modules/nf-core/manta/germline/main.nf | 2 +- tests/modules/nf-core/manta/somatic/main.nf | 2 +- tests/modules/nf-core/manta/tumoronly/main.nf | 2 +- tests/modules/nf-core/mapdamage2/main.nf | 2 +- tests/modules/nf-core/mash/dist/main.nf | 2 +- tests/modules/nf-core/mash/screen/main.nf | 4 ++-- tests/modules/nf-core/mash/sketch/main.nf | 2 +- tests/modules/nf-core/mashtree/main.nf | 2 +- tests/modules/nf-core/maxbin2/main.nf | 2 +- tests/modules/nf-core/maxquant/lfq/main.nf | 2 +- tests/modules/nf-core/mcroni/main.nf | 2 +- tests/modules/nf-core/md5sum/main.nf | 2 +- tests/modules/nf-core/medaka/main.nf | 2 +- tests/modules/nf-core/megahit/main.nf | 2 +- tests/modules/nf-core/megan/daa2info/main.nf | 6 +++--- tests/modules/nf-core/megan/rma2info/main.nf | 2 +- tests/modules/nf-core/meningotype/main.nf | 2 +- tests/modules/nf-core/merqury/main.nf | 6 +++--- .../modules/nf-core/merquryfk/katcomp/main.nf | 6 +++--- tests/modules/nf-core/merquryfk/katgc/main.nf | 4 ++-- .../nf-core/merquryfk/merquryfk/main.nf | 4 ++-- .../nf-core/merquryfk/ploidyplot/main.nf | 4 ++-- tests/modules/nf-core/meryl/count/main.nf | 2 +- tests/modules/nf-core/meryl/histogram/main.nf | 4 ++-- tests/modules/nf-core/meryl/unionsum/main.nf | 4 ++-- .../jgisummarizebamcontigdepths/main.nf | 2 +- .../modules/nf-core/metabat2/metabat2/main.nf | 4 ++-- .../metaphlan3/mergemetaphlantables/main.nf | 6 +++--- .../nf-core/metaphlan3/metaphlan3/main.nf | 4 ++-- .../nf-core/methyldackel/extract/main.nf | 2 +- .../modules/nf-core/methyldackel/mbias/main.nf | 2 +- tests/modules/nf-core/minia/main.nf | 2 +- tests/modules/nf-core/miniasm/main.nf | 2 +- tests/modules/nf-core/minimap2/align/main.nf | 2 +- tests/modules/nf-core/minimap2/index/main.nf | 2 +- tests/modules/nf-core/mlst/main.nf | 2 +- tests/modules/nf-core/mobsuite/recon/main.nf | 2 +- tests/modules/nf-core/mosdepth/main.nf | 10 +++++----- tests/modules/nf-core/motus/downloaddb/main.nf | 2 +- tests/modules/nf-core/motus/merge/main.nf | 8 ++++---- tests/modules/nf-core/motus/profile/main.nf | 4 ++-- tests/modules/nf-core/msisensor/msi/main.nf | 4 ++-- tests/modules/nf-core/msisensor/scan/main.nf | 2 +- tests/modules/nf-core/msisensor2/msi/main.nf | 4 ++-- tests/modules/nf-core/msisensor2/scan/main.nf | 2 +- .../nf-core/msisensorpro/msi_somatic/main.nf | 4 ++-- .../modules/nf-core/msisensorpro/scan/main.nf | 2 +- tests/modules/nf-core/mtnucratio/main.nf | 2 +- tests/modules/nf-core/multiqc/main.nf | 6 +++--- tests/modules/nf-core/multivcfanalyzer/main.nf | 6 +++--- tests/modules/nf-core/mummer/main.nf | 2 +- tests/modules/nf-core/muscle/main.nf | 4 ++-- tests/modules/nf-core/mykrobe/predict/main.nf | 2 +- tests/modules/nf-core/nanolyse/main.nf | 2 +- tests/modules/nf-core/nanoplot/main.nf | 2 +- .../modules/nf-core/ncbigenomedownload/main.nf | 2 +- .../nf-core/nextclade/datasetget/main.nf | 2 +- tests/modules/nf-core/nextclade/run/main.nf | 4 ++-- tests/modules/nf-core/nextgenmap/main.nf | 2 +- tests/modules/nf-core/ngmaster/main.nf | 2 +- tests/modules/nf-core/ngscheckmate/ncm/main.nf | 10 +++++----- tests/modules/nf-core/nucmer/main.nf | 2 +- tests/modules/nf-core/optitype/main.nf | 2 +- tests/modules/nf-core/pairix/main.nf | 2 +- tests/modules/nf-core/pairtools/dedup/main.nf | 2 +- tests/modules/nf-core/pairtools/flip/main.nf | 2 +- tests/modules/nf-core/pairtools/parse/main.nf | 2 +- .../modules/nf-core/pairtools/restrict/main.nf | 2 +- tests/modules/nf-core/pairtools/select/main.nf | 2 +- tests/modules/nf-core/pairtools/sort/main.nf | 2 +- tests/modules/nf-core/panaroo/run/main.nf | 2 +- tests/modules/nf-core/pangolin/main.nf | 2 +- tests/modules/nf-core/paraclu/main.nf | 2 +- tests/modules/nf-core/pasty/main.nf | 2 +- tests/modules/nf-core/pbbam/pbmerge/main.nf | 2 +- tests/modules/nf-core/pbccs/main.nf | 2 +- tests/modules/nf-core/pbptyper/main.nf | 2 +- tests/modules/nf-core/pear/main.nf | 2 +- tests/modules/nf-core/peddy/main.nf | 2 +- .../nf-core/phantompeakqualtools/main.nf | 2 +- tests/modules/nf-core/phyloflash/main.nf | 2 +- .../picard/addorreplacereadgroups/main.nf | 2 +- tests/modules/nf-core/picard/cleansam/main.nf | 2 +- .../nf-core/picard/collecthsmetrics/main.nf | 2 +- .../picard/collectmultiplemetrics/main.nf | 2 +- .../nf-core/picard/collectwgsmetrics/main.nf | 2 +- .../picard/createsequencedictionary/main.nf | 2 +- .../picard/crosscheckfingerprints/main.nf | 2 +- .../modules/nf-core/picard/fastqtosam/main.nf | 2 +- .../nf-core/picard/filtersamreads/main.nf | 4 ++-- .../nf-core/picard/fixmateinformation/main.nf | 2 +- .../modules/nf-core/picard/liftovervcf/main.nf | 2 +- .../nf-core/picard/markduplicates/main.nf | 4 ++-- .../nf-core/picard/mergesamfiles/main.nf | 2 +- tests/modules/nf-core/picard/sortsam/main.nf | 2 +- tests/modules/nf-core/picard/sortvcf/main.nf | 2 +- 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tests/modules/nf-core/samtools/getrg/main.nf | 2 +- .../modules/nf-core/samtools/idxstats/main.nf | 2 +- tests/modules/nf-core/samtools/index/main.nf | 6 +++--- tests/modules/nf-core/samtools/markdup/main.nf | 8 ++++---- tests/modules/nf-core/samtools/merge/main.nf | 2 +- tests/modules/nf-core/samtools/mpileup/main.nf | 2 +- tests/modules/nf-core/samtools/sort/main.nf | 2 +- tests/modules/nf-core/samtools/stats/main.nf | 2 +- tests/modules/nf-core/samtools/view/main.nf | 2 +- tests/modules/nf-core/scoary/main.nf | 2 +- .../nf-core/scramble/clusteranalysis/main.nf | 4 ++-- .../nf-core/scramble/clusteridentifier/main.nf | 2 +- tests/modules/nf-core/seacr/callpeak/main.nf | 2 +- tests/modules/nf-core/seqkit/pair/main.nf | 2 +- tests/modules/nf-core/seqkit/replace/main.nf | 4 ++-- tests/modules/nf-core/seqkit/split2/main.nf | 6 +++--- tests/modules/nf-core/seqkit/stats/main.nf | 2 +- tests/modules/nf-core/seqsero2/main.nf | 2 +- tests/modules/nf-core/seqtk/mergepe/main.nf | 2 +- tests/modules/nf-core/seqtk/rename/main.nf | 2 +- tests/modules/nf-core/seqtk/sample/main.nf | 2 +- tests/modules/nf-core/seqtk/seq/main.nf | 2 +- tests/modules/nf-core/seqtk/subseq/main.nf | 2 +- .../nf-core/sequenzautils/bam2seqz/main.nf | 2 +- .../nf-core/sequenzautils/gcwiggle/main.nf | 2 +- tests/modules/nf-core/seqwish/induce/main.nf | 2 +- tests/modules/nf-core/seroba/run/main.nf | 2 +- tests/modules/nf-core/sexdeterrmine/main.nf | 4 ++-- tests/modules/nf-core/shasta/main.nf | 2 +- tests/modules/nf-core/shasum/main.nf | 2 +- tests/modules/nf-core/shigatyper/main.nf | 2 +- tests/modules/nf-core/shovill/main.nf | 8 ++++---- tests/modules/nf-core/sistr/main.nf | 2 +- tests/modules/nf-core/slimfastq/main.nf | 2 +- .../modules/nf-core/snapaligner/align/main.nf | 4 ++-- .../modules/nf-core/snapaligner/index/main.nf | 2 +- tests/modules/nf-core/snippy/core/main.nf | 4 ++-- tests/modules/nf-core/snippy/run/main.nf | 2 +- tests/modules/nf-core/snpdists/main.nf | 2 +- tests/modules/nf-core/snpeff/main.nf | 2 +- tests/modules/nf-core/snpsift/split/main.nf | 2 +- tests/modules/nf-core/snpsites/main.nf | 2 +- tests/modules/nf-core/somalier/extract/main.nf | 2 +- tests/modules/nf-core/somalier/relate/main.nf | 2 +- tests/modules/nf-core/sourmash/sketch/main.nf | 2 +- tests/modules/nf-core/spades/main.nf | 2 +- tests/modules/nf-core/spatyper/main.nf | 4 ++-- .../nf-core/sratools/fasterqdump/main.nf | 4 ++-- .../modules/nf-core/sratools/prefetch/main.nf | 2 +- tests/modules/nf-core/srst2/srst2/main.nf | 2 +- tests/modules/nf-core/ssuissero/main.nf | 2 +- .../nf-core/stadeniolib/scramble/main.nf | 2 +- tests/modules/nf-core/staphopiasccmec/main.nf | 4 ++-- tests/modules/nf-core/star/align/main.nf | 8 ++++---- .../nf-core/star/genomegenerate/main.nf | 2 +- tests/modules/nf-core/stranger/main.nf | 4 ++-- tests/modules/nf-core/strelka/germline/main.nf | 2 +- tests/modules/nf-core/strelka/somatic/main.nf | 2 +- tests/modules/nf-core/stringtie/merge/main.nf | 4 ++-- .../nf-core/stringtie/stringtie/main.nf | 2 +- .../nf-core/subread/featurecounts/main.nf | 2 +- tests/modules/nf-core/svdb/merge/main.nf | 2 +- tests/modules/nf-core/svdb/query/main.nf | 2 +- tests/modules/nf-core/svtk/standardize/main.nf | 4 ++-- tests/modules/nf-core/tabix/bgzip/main.nf | 4 ++-- tests/modules/nf-core/tabix/bgziptabix/main.nf | 2 +- tests/modules/nf-core/tabix/tabix/main.nf | 8 ++++---- tests/modules/nf-core/tailfindr/main.nf | 2 +- .../modules/nf-core/tbprofiler/profile/main.nf | 2 +- tests/modules/nf-core/tiddit/cov/main.nf | 4 ++-- tests/modules/nf-core/tiddit/sv/main.nf | 6 +++--- .../nf-core/transdecoder/longorf/main.nf | 2 +- .../nf-core/transdecoder/predict/main.nf | 4 ++-- tests/modules/nf-core/trimgalore/main.nf | 2 +- tests/modules/nf-core/trimmomatic/main.nf | 2 +- tests/modules/nf-core/ucsc/bedclip/main.nf | 2 +- .../nf-core/ucsc/bedgraphtobigwig/main.nf | 2 +- tests/modules/nf-core/ucsc/bedtobigbed/main.nf | 4 ++-- .../nf-core/ucsc/bigwigaverageoverbed/main.nf | 2 +- tests/modules/nf-core/ucsc/liftover/main.nf | 2 +- tests/modules/nf-core/ucsc/wigtobigwig/main.nf | 2 +- tests/modules/nf-core/ultra/align/main.nf | 8 ++++---- tests/modules/nf-core/ultra/index/main.nf | 4 ++-- tests/modules/nf-core/ultra/pipeline/main.nf | 6 +++--- tests/modules/nf-core/umitools/dedup/main.nf | 10 +++++----- tests/modules/nf-core/umitools/extract/main.nf | 2 +- tests/modules/nf-core/unicycler/main.nf | 2 +- tests/modules/nf-core/untar/main.nf | 2 +- tests/modules/nf-core/unzip/main.nf | 2 +- tests/modules/nf-core/vardictjava/main.nf | 2 +- tests/modules/nf-core/variantbam/main.nf | 2 +- tests/modules/nf-core/vcf2db/main.nf | 2 +- tests/modules/nf-core/vcf2maf/main.nf | 4 ++-- tests/modules/nf-core/vcfanno/main.nf | 4 ++-- .../nf-core/vcflib/vcfbreakmulti/main.nf | 2 +- tests/modules/nf-core/vcflib/vcfuniq/main.nf | 2 +- tests/modules/nf-core/vcftools/main.nf | 4 ++-- tests/modules/nf-core/vsearch/sintax/main.nf | 2 +- .../nf-core/vsearch/usearchglobal/main.nf | 2 +- tests/modules/nf-core/whamg/main.nf | 2 +- tests/modules/nf-core/yara/index/main.nf | 2 +- tests/modules/nf-core/yara/mapper/main.nf | 4 ++-- 631 files changed, 968 insertions(+), 968 deletions(-) diff --git a/tests/modules/nf-core/abacas/main.nf b/tests/modules/nf-core/abacas/main.nf index 7115c292d72..ee1a56b22b9 100644 --- a/tests/modules/nf-core/abacas/main.nf +++ b/tests/modules/nf-core/abacas/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ABACAS } from '../../../modules/nf-core/abacas/main.nf' +include { ABACAS } from '../../../../modules/nf-core/abacas/main.nf' workflow test_abacas { diff --git a/tests/modules/nf-core/abricate/run/main.nf b/tests/modules/nf-core/abricate/run/main.nf index 2f15aaba3b6..b8c2efa239a 100644 --- a/tests/modules/nf-core/abricate/run/main.nf +++ b/tests/modules/nf-core/abricate/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ABRICATE_RUN } from '../../../../modules/nf-core/abricate/run/main.nf' +include { ABRICATE_RUN } from '../../../../../modules/nf-core/abricate/run/main.nf' workflow test_abricate_run { diff --git a/tests/modules/nf-core/abricate/summary/main.nf b/tests/modules/nf-core/abricate/summary/main.nf index d6f92a6ad33..aa545408287 100644 --- a/tests/modules/nf-core/abricate/summary/main.nf +++ b/tests/modules/nf-core/abricate/summary/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ABRICATE_RUN } from '../../../../modules/nf-core/abricate/run/main.nf' -include { ABRICATE_SUMMARY } from '../../../../modules/nf-core/abricate/summary/main.nf' +include { ABRICATE_RUN } from '../../../../../modules/nf-core/abricate/run/main.nf' +include { ABRICATE_SUMMARY } from '../../../../../modules/nf-core/abricate/summary/main.nf' workflow test_abricate_summary { diff --git a/tests/modules/nf-core/adapterremoval/main.nf b/tests/modules/nf-core/adapterremoval/main.nf index b54c405fa2a..01be917bec1 100644 --- a/tests/modules/nf-core/adapterremoval/main.nf +++ b/tests/modules/nf-core/adapterremoval/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ADAPTERREMOVAL } from '../../../modules/nf-core/adapterremoval/main.nf' -include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../modules/nf-core/adapterremoval/main.nf' +include { ADAPTERREMOVAL } from '../../../../modules/nf-core/adapterremoval/main.nf' +include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../../modules/nf-core/adapterremoval/main.nf' workflow test_adapterremoval_single_end { diff --git a/tests/modules/nf-core/adapterremovalfixprefix/main.nf b/tests/modules/nf-core/adapterremovalfixprefix/main.nf index 10f4a3bebb8..153eae37185 100644 --- a/tests/modules/nf-core/adapterremovalfixprefix/main.nf +++ b/tests/modules/nf-core/adapterremovalfixprefix/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ADAPTERREMOVAL } from '../../../modules/nf-core/adapterremoval/main.nf' -include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/nf-core/adapterremovalfixprefix/main.nf' +include { ADAPTERREMOVAL } from '../../../../modules/nf-core/adapterremoval/main.nf' +include { ADAPTERREMOVALFIXPREFIX } from '../../../../modules/nf-core/adapterremovalfixprefix/main.nf' workflow test_adapterremovalfixprefix { diff --git a/tests/modules/nf-core/agrvate/main.nf b/tests/modules/nf-core/agrvate/main.nf index 069a800562c..d19d110cf04 100644 --- a/tests/modules/nf-core/agrvate/main.nf +++ b/tests/modules/nf-core/agrvate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { AGRVATE } from '../../../modules/nf-core/agrvate/main.nf' +include { AGRVATE } from '../../../../modules/nf-core/agrvate/main.nf' workflow test_agrvate { diff --git a/tests/modules/nf-core/allelecounter/main.nf b/tests/modules/nf-core/allelecounter/main.nf index 380d7d9340a..4925aa94998 100644 --- a/tests/modules/nf-core/allelecounter/main.nf +++ b/tests/modules/nf-core/allelecounter/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { ALLELECOUNTER } from '../../../modules/nf-core/allelecounter/main.nf' +include { ALLELECOUNTER } from '../../../../modules/nf-core/allelecounter/main.nf' workflow test_allelecounter_bam { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/ampir/main.nf b/tests/modules/nf-core/ampir/main.nf index 76d4fda112f..0628795cc97 100644 --- a/tests/modules/nf-core/ampir/main.nf +++ b/tests/modules/nf-core/ampir/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { AMPIR } from '../../../modules/nf-core/ampir/main.nf' +include { AMPIR } from '../../../../modules/nf-core/ampir/main.nf' workflow test_ampir { diff --git a/tests/modules/nf-core/amplify/predict/main.nf b/tests/modules/nf-core/amplify/predict/main.nf index 1c55561676d..e8b3b5df525 100644 --- a/tests/modules/nf-core/amplify/predict/main.nf +++ b/tests/modules/nf-core/amplify/predict/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PRODIGAL } from '../../../modules/nf-core/prodigal/main.nf' addParams( options: [:] ) -include { AMPLIFY_PREDICT } from '../../../../modules/nf-core/amplify/predict/main.nf' addParams( options: [:] ) +include { PRODIGAL } from '../../../../modules/nf-core/prodigal/main.nf' addParams( options: [:] ) +include { AMPLIFY_PREDICT } from '../../../../../modules/nf-core/amplify/predict/main.nf' addParams( options: [:] ) workflow amplify_predict { diff --git a/tests/modules/nf-core/amps/main.nf b/tests/modules/nf-core/amps/main.nf index 53eeda2df03..e0615367a86 100644 --- a/tests/modules/nf-core/amps/main.nf +++ b/tests/modules/nf-core/amps/main.nf @@ -2,12 +2,12 @@ nextflow.enable.dsl = 2 -include { UNZIP as UNZIP_MALT } from '../../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/nf-core/unzip/main.nf' -include { MALT_BUILD } from '../../../modules/nf-core/malt/build/main.nf' -include { MALT_RUN } from '../../../modules/nf-core/malt/run/main.nf' -include { MALTEXTRACT } from '../../../modules/nf-core/maltextract/main.nf' -include { AMPS } from '../../../modules/nf-core/amps/main.nf' +include { UNZIP as UNZIP_MALT } from '../../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_MALTEXTRACT } from '../../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../../modules/nf-core/malt/build/main.nf' +include { MALT_RUN } from '../../../../modules/nf-core/malt/run/main.nf' +include { MALTEXTRACT } from '../../../../modules/nf-core/maltextract/main.nf' +include { AMPS } from '../../../../modules/nf-core/amps/main.nf' workflow test_amps { diff --git a/tests/modules/nf-core/amrfinderplus/run/main.nf b/tests/modules/nf-core/amrfinderplus/run/main.nf index 8e807301b70..0f887457fc2 100644 --- a/tests/modules/nf-core/amrfinderplus/run/main.nf +++ b/tests/modules/nf-core/amrfinderplus/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { AMRFINDERPLUS_UPDATE } from '../../../../modules/nf-core/amrfinderplus/update/main.nf' -include { AMRFINDERPLUS_RUN } from '../../../../modules/nf-core/amrfinderplus/run/main.nf' +include { AMRFINDERPLUS_UPDATE } from '../../../../../modules/nf-core/amrfinderplus/update/main.nf' +include { AMRFINDERPLUS_RUN } from '../../../../../modules/nf-core/amrfinderplus/run/main.nf' workflow test_amrfinderplus_run { diff --git a/tests/modules/nf-core/amrfinderplus/update/main.nf b/tests/modules/nf-core/amrfinderplus/update/main.nf index 08f4060f84f..4f5c73cfafa 100644 --- a/tests/modules/nf-core/amrfinderplus/update/main.nf +++ b/tests/modules/nf-core/amrfinderplus/update/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { AMRFINDERPLUS_UPDATE } from '../../../../modules/nf-core/amrfinderplus/update/main.nf' +include { AMRFINDERPLUS_UPDATE } from '../../../../../modules/nf-core/amrfinderplus/update/main.nf' workflow test_amrfinderplus_update { diff --git a/tests/modules/nf-core/angsd/docounts/main.nf b/tests/modules/nf-core/angsd/docounts/main.nf index e6960bb8bac..2188a097c03 100644 --- a/tests/modules/nf-core/angsd/docounts/main.nf +++ b/tests/modules/nf-core/angsd/docounts/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ANGSD_DOCOUNTS } from '../../../../modules/nf-core/angsd/docounts/main.nf' +include { ANGSD_DOCOUNTS } from '../../../../../modules/nf-core/angsd/docounts/main.nf' workflow test_angsd_docounts { diff --git a/tests/modules/nf-core/antismash/antismashlite/main.nf b/tests/modules/nf-core/antismash/antismashlite/main.nf index 258654fcedd..73c55dc8bcb 100644 --- a/tests/modules/nf-core/antismash/antismashlite/main.nf +++ b/tests/modules/nf-core/antismash/antismashlite/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/nf-core/antismash/antismashlite/main.nf' -include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf' -include { GUNZIP as GUNZIP1 } from '../../../../modules/nf-core/gunzip/main.nf' -include { GUNZIP as GUNZIP2 } from '../../../../modules/nf-core/gunzip/main.nf' -include { UNTAR as UNTAR1 } from '../../../../modules/nf-core/untar/main.nf' -include { UNTAR as UNTAR2 } from '../../../../modules/nf-core/untar/main.nf' -include { UNTAR as UNTAR3 } from '../../../../modules/nf-core/untar/main.nf' +include { ANTISMASH_ANTISMASHLITE } from '../../../../../modules/nf-core/antismash/antismashlite/main.nf' +include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf' +include { GUNZIP as GUNZIP1 } from '../../../../../modules/nf-core/gunzip/main.nf' +include { GUNZIP as GUNZIP2 } from '../../../../../modules/nf-core/gunzip/main.nf' +include { UNTAR as UNTAR1 } from '../../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR2 } from '../../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR3 } from '../../../../../modules/nf-core/untar/main.nf' workflow test_antismashlite { genome_fna = [ diff --git a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index 5faf2111639..9d91eea4d65 100644 --- a/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { UNTAR as UNTAR1 } from '../../../../modules/nf-core/untar/main.nf' -include { UNTAR as UNTAR2 } from '../../../../modules/nf-core/untar/main.nf' -include { UNTAR as UNTAR3 } from '../../../../modules/nf-core/untar/main.nf' -include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf' +include { UNTAR as UNTAR1 } from '../../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR2 } from '../../../../../modules/nf-core/untar/main.nf' +include { UNTAR as UNTAR3 } from '../../../../../modules/nf-core/untar/main.nf' +include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf' workflow test_antismash_antismashlitedownloaddatabases { input1 = [ diff --git a/tests/modules/nf-core/ariba/getref/main.nf b/tests/modules/nf-core/ariba/getref/main.nf index f5d32fc0cd1..6cbcb251415 100644 --- a/tests/modules/nf-core/ariba/getref/main.nf +++ b/tests/modules/nf-core/ariba/getref/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ARIBA_GETREF } from '../../../../modules/nf-core/ariba/getref/main.nf' +include { ARIBA_GETREF } from '../../../../../modules/nf-core/ariba/getref/main.nf' workflow test_ariba_getref { ARIBA_GETREF ( "card" ) diff --git a/tests/modules/nf-core/ariba/run/main.nf b/tests/modules/nf-core/ariba/run/main.nf index eea3cd12b62..d99362c4477 100644 --- a/tests/modules/nf-core/ariba/run/main.nf +++ b/tests/modules/nf-core/ariba/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ARIBA_GETREF } from '../../../../modules/nf-core/ariba/getref/main.nf' -include { ARIBA_RUN } from '../../../../modules/nf-core/ariba/run/main.nf' +include { ARIBA_GETREF } from '../../../../../modules/nf-core/ariba/getref/main.nf' +include { ARIBA_RUN } from '../../../../../modules/nf-core/ariba/run/main.nf' workflow test_ariba_run { diff --git a/tests/modules/nf-core/arriba/main.nf b/tests/modules/nf-core/arriba/main.nf index c0072d1da3c..17978f4c129 100644 --- a/tests/modules/nf-core/arriba/main.nf +++ b/tests/modules/nf-core/arriba/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main.nf' -include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main.nf' -include { ARRIBA } from '../../../modules/nf-core/arriba/main.nf' +include { STAR_GENOMEGENERATE } from '../../../../modules/nf-core/star/genomegenerate/main.nf' +include { STAR_ALIGN } from '../../../../modules/nf-core/star/align/main.nf' +include { ARRIBA } from '../../../../modules/nf-core/arriba/main.nf' workflow test_arriba_single_end { diff --git a/tests/modules/nf-core/artic/guppyplex/main.nf b/tests/modules/nf-core/artic/guppyplex/main.nf index 83821e4212a..bd60545d1d4 100644 --- a/tests/modules/nf-core/artic/guppyplex/main.nf +++ b/tests/modules/nf-core/artic/guppyplex/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ARTIC_GUPPYPLEX } from '../../../../modules/nf-core/artic/guppyplex/main.nf' +include { ARTIC_GUPPYPLEX } from '../../../../../modules/nf-core/artic/guppyplex/main.nf' process STAGE_FASTQ_DIR { input: diff --git a/tests/modules/nf-core/artic/minion/main.nf b/tests/modules/nf-core/artic/minion/main.nf index 4badfa5d597..4a47f563655 100644 --- a/tests/modules/nf-core/artic/minion/main.nf +++ b/tests/modules/nf-core/artic/minion/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { ARTIC_MINION } from '../../../../modules/nf-core/artic/minion/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { ARTIC_MINION } from '../../../../../modules/nf-core/artic/minion/main.nf' workflow test_artic_minion { diff --git a/tests/modules/nf-core/ascat/main.nf b/tests/modules/nf-core/ascat/main.nf index c2efec3bb14..cf76c6f0b12 100644 --- a/tests/modules/nf-core/ascat/main.nf +++ b/tests/modules/nf-core/ascat/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { ASCAT as ASCAT_SIMPLE } from '../../../modules/nf-core/ascat/main.nf' -include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../modules/nf-core/ascat/main.nf' -include { ASCAT as ASCAT_CRAM } from '../../../modules/nf-core/ascat/main.nf' -include { UNZIP as UNZIP_ALLELES } from '../../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_LOCI } from '../../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_GC } from '../../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_RT } from '../../../modules/nf-core/unzip/main.nf' +include { ASCAT as ASCAT_SIMPLE } from '../../../../modules/nf-core/ascat/main.nf' +include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../../modules/nf-core/ascat/main.nf' +include { ASCAT as ASCAT_CRAM } from '../../../../modules/nf-core/ascat/main.nf' +include { UNZIP as UNZIP_ALLELES } from '../../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_LOCI } from '../../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_GC } from '../../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_RT } from '../../../../modules/nf-core/unzip/main.nf' diff --git a/tests/modules/nf-core/assemblyscan/main.nf b/tests/modules/nf-core/assemblyscan/main.nf index b1fbf954c54..7ad80531fd3 100644 --- a/tests/modules/nf-core/assemblyscan/main.nf +++ b/tests/modules/nf-core/assemblyscan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ASSEMBLYSCAN } from '../../../modules/nf-core/assemblyscan/main.nf' +include { ASSEMBLYSCAN } from '../../../../modules/nf-core/assemblyscan/main.nf' workflow test_assemblyscan { diff --git a/tests/modules/nf-core/ataqv/ataqv/main.nf b/tests/modules/nf-core/ataqv/ataqv/main.nf index a11859df647..9680d68d47a 100644 --- a/tests/modules/nf-core/ataqv/ataqv/main.nf +++ b/tests/modules/nf-core/ataqv/ataqv/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ATAQV_ATAQV } from '../../../../modules/nf-core/ataqv/ataqv/main.nf' -include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../modules/nf-core/ataqv/ataqv/main.nf' +include { ATAQV_ATAQV } from '../../../../../modules/nf-core/ataqv/ataqv/main.nf' +include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../../modules/nf-core/ataqv/ataqv/main.nf' workflow test_ataqv_ataqv { diff --git a/tests/modules/nf-core/ataqv/mkarv/main.nf b/tests/modules/nf-core/ataqv/mkarv/main.nf index 003cb34e06a..f6b05248122 100644 --- a/tests/modules/nf-core/ataqv/mkarv/main.nf +++ b/tests/modules/nf-core/ataqv/mkarv/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ATAQV_ATAQV } from '../../../../modules/nf-core/ataqv/ataqv/main.nf' -include { ATAQV_MKARV } from '../../../../modules/nf-core/ataqv/mkarv/main.nf' +include { ATAQV_ATAQV } from '../../../../../modules/nf-core/ataqv/ataqv/main.nf' +include { ATAQV_MKARV } from '../../../../../modules/nf-core/ataqv/mkarv/main.nf' workflow test_ataqv_mkarv { diff --git a/tests/modules/nf-core/atlas/call/main.nf b/tests/modules/nf-core/atlas/call/main.nf index ed01849d9cf..02c3aaa156a 100644 --- a/tests/modules/nf-core/atlas/call/main.nf +++ b/tests/modules/nf-core/atlas/call/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_CALL } from '../../../../modules/nf-core/atlas/call/main.nf' +include { ATLAS_CALL } from '../../../../../modules/nf-core/atlas/call/main.nf' workflow test_atlas_call { diff --git a/tests/modules/nf-core/atlas/pmd/main.nf b/tests/modules/nf-core/atlas/pmd/main.nf index 26d8d2e5fb1..bcba7dc3f4f 100644 --- a/tests/modules/nf-core/atlas/pmd/main.nf +++ b/tests/modules/nf-core/atlas/pmd/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_PMD } from '../../../../modules/nf-core/atlas/pmd/main.nf' +include { ATLAS_PMD } from '../../../../../modules/nf-core/atlas/pmd/main.nf' workflow test_atlas_pmd { diff --git a/tests/modules/nf-core/atlas/recal/main.nf b/tests/modules/nf-core/atlas/recal/main.nf index df69f99873d..fadda2019e6 100644 --- a/tests/modules/nf-core/atlas/recal/main.nf +++ b/tests/modules/nf-core/atlas/recal/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_RECAL } from '../../../../modules/nf-core/atlas/recal/main.nf' +include { ATLAS_RECAL } from '../../../../../modules/nf-core/atlas/recal/main.nf' workflow test_atlas_recal { diff --git a/tests/modules/nf-core/atlas/splitmerge/main.nf b/tests/modules/nf-core/atlas/splitmerge/main.nf index 10f6058ce76..bde3c197329 100644 --- a/tests/modules/nf-core/atlas/splitmerge/main.nf +++ b/tests/modules/nf-core/atlas/splitmerge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ATLAS_SPLITMERGE } from '../../../../modules/nf-core/atlas/splitmerge/main.nf' +include { ATLAS_SPLITMERGE } from '../../../../../modules/nf-core/atlas/splitmerge/main.nf' //MAIN workflow test_atlas_splitmerge { diff --git a/tests/modules/nf-core/bakta/main.nf b/tests/modules/nf-core/bakta/main.nf index c9221b6b7a2..659d235705c 100644 --- a/tests/modules/nf-core/bakta/main.nf +++ b/tests/modules/nf-core/bakta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAKTA } from '../../../modules/nf-core/bakta/main.nf' +include { BAKTA } from '../../../../modules/nf-core/bakta/main.nf' workflow test_bakta { diff --git a/tests/modules/nf-core/bamaligncleaner/main.nf b/tests/modules/nf-core/bamaligncleaner/main.nf index b7072779a79..a84d410a476 100644 --- a/tests/modules/nf-core/bamaligncleaner/main.nf +++ b/tests/modules/nf-core/bamaligncleaner/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAMALIGNCLEANER } from '../../../modules/nf-core/bamaligncleaner/main.nf' +include { BAMALIGNCLEANER } from '../../../../modules/nf-core/bamaligncleaner/main.nf' workflow test_bamaligncleaner { diff --git a/tests/modules/nf-core/bamcmp/main.nf b/tests/modules/nf-core/bamcmp/main.nf index 279dd92d063..85d0dc5ad3c 100644 --- a/tests/modules/nf-core/bamcmp/main.nf +++ b/tests/modules/nf-core/bamcmp/main.nf @@ -2,15 +2,15 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../modules/nf-core/bwa/index/main.nf' -include { BWA_MEM } from '../../../modules/nf-core/bwa/mem/main.nf' -include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../modules/nf-core/bwa/index/main.nf' -include { BWA_MEM as BWA_MEM_COV2 } from '../../../modules/nf-core/bwa/mem/main.nf' +include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM } from '../../../../modules/nf-core/bwa/mem/main.nf' +include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM as BWA_MEM_COV2 } from '../../../../modules/nf-core/bwa/mem/main.nf' -include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main.nf' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2 } from '../../../modules/nf-core/samtools/sort/main.nf' +include { SAMTOOLS_SORT } from '../../../../modules/nf-core/samtools/sort/main.nf' +include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2 } from '../../../../modules/nf-core/samtools/sort/main.nf' -include { BAMCMP } from '../../../modules/nf-core/bamcmp/main.nf' +include { BAMCMP } from '../../../../modules/nf-core/bamcmp/main.nf' workflow test_bamcmp { diff --git a/tests/modules/nf-core/bamtools/convert/main.nf b/tests/modules/nf-core/bamtools/convert/main.nf index f719f615969..e4bbfb61b8b 100644 --- a/tests/modules/nf-core/bamtools/convert/main.nf +++ b/tests/modules/nf-core/bamtools/convert/main.nf @@ -2,15 +2,15 @@ nextflow.enable.dsl = 2 -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/nf-core/bamtools/convert/main.nf' -include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../../modules/nf-core/bamtools/convert/main.nf' +include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../../modules/nf-core/bamtools/convert/main.nf' workflow test_bamtools_convert_ext_error { diff --git a/tests/modules/nf-core/bamtools/split/main.nf b/tests/modules/nf-core/bamtools/split/main.nf index ea0e46ef51a..504ecef4bbd 100644 --- a/tests/modules/nf-core/bamtools/split/main.nf +++ b/tests/modules/nf-core/bamtools/split/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE } from '../../../../modules/nf-core/bamtools/split/main.nf' -include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/nf-core/bamtools/split/main.nf' +include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE } from '../../../../../modules/nf-core/bamtools/split/main.nf' +include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../../modules/nf-core/bamtools/split/main.nf' workflow test_bamtools_split_single_input { diff --git a/tests/modules/nf-core/bamtools/stats/main.nf b/tests/modules/nf-core/bamtools/stats/main.nf index 38aea055e49..6adbb060bea 100644 --- a/tests/modules/nf-core/bamtools/stats/main.nf +++ b/tests/modules/nf-core/bamtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAMTOOLS_STATS } from '../../../../modules/nf-core/bamtools/stats/main.nf' +include { BAMTOOLS_STATS } from '../../../../../modules/nf-core/bamtools/stats/main.nf' workflow test_bamtools_stats { diff --git a/tests/modules/nf-core/bamutil/trimbam/main.nf b/tests/modules/nf-core/bamutil/trimbam/main.nf index 659e9d7d6bf..b2359338d88 100644 --- a/tests/modules/nf-core/bamutil/trimbam/main.nf +++ b/tests/modules/nf-core/bamutil/trimbam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAMUTIL_TRIMBAM } from '../../../../modules/nf-core/bamutil/trimbam/main.nf' +include { BAMUTIL_TRIMBAM } from '../../../../../modules/nf-core/bamutil/trimbam/main.nf' workflow test_bamutil_trimbam { diff --git a/tests/modules/nf-core/bandage/image/main.nf b/tests/modules/nf-core/bandage/image/main.nf index a5eea45be03..3da08d40bc0 100644 --- a/tests/modules/nf-core/bandage/image/main.nf +++ b/tests/modules/nf-core/bandage/image/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BANDAGE_IMAGE } from '../../../../modules/nf-core/bandage/image/main.nf' +include { BANDAGE_IMAGE } from '../../../../../modules/nf-core/bandage/image/main.nf' workflow test_bandage_image { input = [ diff --git a/tests/modules/nf-core/bases2fastq/main.nf b/tests/modules/nf-core/bases2fastq/main.nf index af6b8e3e419..d9fdac02715 100644 --- a/tests/modules/nf-core/bases2fastq/main.nf +++ b/tests/modules/nf-core/bases2fastq/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BASES2FASTQ } from '../../../modules/nf-core/bases2fastq/main.nf' -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { BASES2FASTQ } from '../../../../modules/nf-core/bases2fastq/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_bases2fastq { diff --git a/tests/modules/nf-core/bbmap/align/main.nf b/tests/modules/nf-core/bbmap/align/main.nf index 8e816212fd1..f2bfcd9069c 100644 --- a/tests/modules/nf-core/bbmap/align/main.nf +++ b/tests/modules/nf-core/bbmap/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BBMAP_INDEX } from '../../../../modules/nf-core/bbmap/index/main.nf' -include { BBMAP_ALIGN } from '../../../../modules/nf-core/bbmap/align/main.nf' -include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/nf-core/bbmap/align/main.nf' +include { BBMAP_INDEX } from '../../../../../modules/nf-core/bbmap/index/main.nf' +include { BBMAP_ALIGN } from '../../../../../modules/nf-core/bbmap/align/main.nf' +include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../../modules/nf-core/bbmap/align/main.nf' workflow test_bbmap_align_paired_end_fasta_ref { diff --git a/tests/modules/nf-core/bbmap/bbduk/main.nf b/tests/modules/nf-core/bbmap/bbduk/main.nf index 452dae2adcc..a0e8c57d9c8 100644 --- a/tests/modules/nf-core/bbmap/bbduk/main.nf +++ b/tests/modules/nf-core/bbmap/bbduk/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_BBDUK } from '../../../../modules/nf-core/bbmap/bbduk/main.nf' +include { BBMAP_BBDUK } from '../../../../../modules/nf-core/bbmap/bbduk/main.nf' workflow test_bbmap_bbduk_single_end { diff --git a/tests/modules/nf-core/bbmap/bbsplit/main.nf b/tests/modules/nf-core/bbmap/bbsplit/main.nf index 7960dbe7e52..ede4b7d0bef 100644 --- a/tests/modules/nf-core/bbmap/bbsplit/main.nf +++ b/tests/modules/nf-core/bbmap/bbsplit/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/nf-core/bbmap/bbsplit/main.nf' -include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/nf-core/bbmap/bbsplit/main.nf' +include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../../modules/nf-core/bbmap/bbsplit/main.nf' +include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../../modules/nf-core/bbmap/bbsplit/main.nf' workflow test_bbmap_bbsplit { diff --git a/tests/modules/nf-core/bbmap/clumpify/main.nf b/tests/modules/nf-core/bbmap/clumpify/main.nf index 77c776c5a44..65b49acce8e 100644 --- a/tests/modules/nf-core/bbmap/clumpify/main.nf +++ b/tests/modules/nf-core/bbmap/clumpify/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_CLUMPIFY } from '../../../../modules/nf-core/bbmap/clumpify/main.nf' +include { BBMAP_CLUMPIFY } from '../../../../../modules/nf-core/bbmap/clumpify/main.nf' workflow test_bbmap_clumpify_single_end { diff --git a/tests/modules/nf-core/bbmap/index/main.nf b/tests/modules/nf-core/bbmap/index/main.nf index 811100e8fc3..1c1ad0f422e 100644 --- a/tests/modules/nf-core/bbmap/index/main.nf +++ b/tests/modules/nf-core/bbmap/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_INDEX } from '../../../../modules/nf-core/bbmap/index/main.nf' +include { BBMAP_INDEX } from '../../../../../modules/nf-core/bbmap/index/main.nf' workflow test_bbmap_index { diff --git a/tests/modules/nf-core/bbmap/pileup/main.nf b/tests/modules/nf-core/bbmap/pileup/main.nf index d63b8c426be..beb482abfce 100644 --- a/tests/modules/nf-core/bbmap/pileup/main.nf +++ b/tests/modules/nf-core/bbmap/pileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BBMAP_PILEUP } from '../../../../modules/nf-core/bbmap/pileup/main.nf' +include { BBMAP_PILEUP } from '../../../../../modules/nf-core/bbmap/pileup/main.nf' workflow test_bbmap_pileup { diff --git a/tests/modules/nf-core/bcftools/annotate/main.nf b/tests/modules/nf-core/bcftools/annotate/main.nf index 2b2a620a90b..df59b6465c9 100644 --- a/tests/modules/nf-core/bcftools/annotate/main.nf +++ b/tests/modules/nf-core/bcftools/annotate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_ANNOTATE } from '../../../../modules/nf-core/bcftools/annotate/main.nf' +include { BCFTOOLS_ANNOTATE } from '../../../../../modules/nf-core/bcftools/annotate/main.nf' workflow test_bcftools_annotate_out_vcf { diff --git a/tests/modules/nf-core/bcftools/concat/main.nf b/tests/modules/nf-core/bcftools/concat/main.nf index 3455f9a28e7..582af6db550 100644 --- a/tests/modules/nf-core/bcftools/concat/main.nf +++ b/tests/modules/nf-core/bcftools/concat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONCAT } from '../../../../modules/nf-core/bcftools/concat/main.nf' +include { BCFTOOLS_CONCAT } from '../../../../../modules/nf-core/bcftools/concat/main.nf' workflow test_bcftools_concat_tbi { diff --git a/tests/modules/nf-core/bcftools/consensus/main.nf b/tests/modules/nf-core/bcftools/consensus/main.nf index 431946ed4cd..ffc3c5f9545 100644 --- a/tests/modules/nf-core/bcftools/consensus/main.nf +++ b/tests/modules/nf-core/bcftools/consensus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONSENSUS } from '../../../../modules/nf-core/bcftools/consensus/main.nf' +include { BCFTOOLS_CONSENSUS } from '../../../../../modules/nf-core/bcftools/consensus/main.nf' workflow test_bcftools_consensus { diff --git a/tests/modules/nf-core/bcftools/convert/main.nf b/tests/modules/nf-core/bcftools/convert/main.nf index f7e2276bb70..5ea3c9a52bb 100644 --- a/tests/modules/nf-core/bcftools/convert/main.nf +++ b/tests/modules/nf-core/bcftools/convert/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../modules/nf-core/bcftools/convert/main.nf' -include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF } from '../../../../modules/nf-core/bcftools/convert/main.nf' +include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_GVCF } from '../../../../../modules/nf-core/bcftools/convert/main.nf' +include { BCFTOOLS_CONVERT as BCFTOOLS_CONVERT_BCF } from '../../../../../modules/nf-core/bcftools/convert/main.nf' workflow test_bcftools_convert_gvcf { diff --git a/tests/modules/nf-core/bcftools/filter/main.nf b/tests/modules/nf-core/bcftools/filter/main.nf index bf1fb3b52d4..0fff20eb406 100644 --- a/tests/modules/nf-core/bcftools/filter/main.nf +++ b/tests/modules/nf-core/bcftools/filter/main.nf @@ -3,7 +3,7 @@ nextflow.enable.dsl = 2 //keep --no-verson argument, otherwise md5 will change on each execution -include { BCFTOOLS_FILTER } from '../../../../modules/nf-core/bcftools/filter/main.nf' +include { BCFTOOLS_FILTER } from '../../../../../modules/nf-core/bcftools/filter/main.nf' workflow test_bcftools_filter { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/index/main.nf b/tests/modules/nf-core/bcftools/index/main.nf index 35228bcd608..ba58f4076d7 100644 --- a/tests/modules/nf-core/bcftools/index/main.nf +++ b/tests/modules/nf-core/bcftools/index/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../modules/nf-core/bcftools/index/main.nf' -include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../modules/nf-core/bcftools/index/main.nf' +include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../../modules/nf-core/bcftools/index/main.nf' +include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../../modules/nf-core/bcftools/index/main.nf' workflow test_bcftools_index_csi { diff --git a/tests/modules/nf-core/bcftools/isec/main.nf b/tests/modules/nf-core/bcftools/isec/main.nf index e75cc3dd15e..42012448d2c 100644 --- a/tests/modules/nf-core/bcftools/isec/main.nf +++ b/tests/modules/nf-core/bcftools/isec/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_ISEC } from '../../../../modules/nf-core/bcftools/isec/main.nf' +include { BCFTOOLS_ISEC } from '../../../../../modules/nf-core/bcftools/isec/main.nf' workflow test_bcftools_isec { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/merge/main.nf b/tests/modules/nf-core/bcftools/merge/main.nf index 7a0f10e813f..2b3df3f4d32 100644 --- a/tests/modules/nf-core/bcftools/merge/main.nf +++ b/tests/modules/nf-core/bcftools/merge/main.nf @@ -3,9 +3,9 @@ nextflow.enable.dsl = 2 //keep --no-verson argument, otherwise md5 will change on each execution -include { BCFTOOLS_MERGE } from '../../../../modules/nf-core/bcftools/merge/main.nf' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../modules/nf-core/bcftools/merge/main.nf' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF } from '../../../../modules/nf-core/bcftools/merge/main.nf' +include { BCFTOOLS_MERGE } from '../../../../../modules/nf-core/bcftools/merge/main.nf' +include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_GVCF } from '../../../../../modules/nf-core/bcftools/merge/main.nf' +include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_BCF } from '../../../../../modules/nf-core/bcftools/merge/main.nf' workflow test_bcftools_merge { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/mpileup/main.nf b/tests/modules/nf-core/bcftools/mpileup/main.nf index 33e02842572..02da43cc9c6 100644 --- a/tests/modules/nf-core/bcftools/mpileup/main.nf +++ b/tests/modules/nf-core/bcftools/mpileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_MPILEUP } from '../../../../modules/nf-core/bcftools/mpileup/main.nf' +include { BCFTOOLS_MPILEUP } from '../../../../../modules/nf-core/bcftools/mpileup/main.nf' workflow test_bcftools_mpileup { diff --git a/tests/modules/nf-core/bcftools/norm/main.nf b/tests/modules/nf-core/bcftools/norm/main.nf index cf667d65ade..53363bec82b 100644 --- a/tests/modules/nf-core/bcftools/norm/main.nf +++ b/tests/modules/nf-core/bcftools/norm/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_NORM } from '../../../../modules/nf-core/bcftools/norm/main.nf' +include { BCFTOOLS_NORM } from '../../../../../modules/nf-core/bcftools/norm/main.nf' workflow test_bcftools_norm_no_tbi { diff --git a/tests/modules/nf-core/bcftools/query/main.nf b/tests/modules/nf-core/bcftools/query/main.nf index 057a4f7c882..d1ad7e96aae 100644 --- a/tests/modules/nf-core/bcftools/query/main.nf +++ b/tests/modules/nf-core/bcftools/query/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_QUERY } from '../../../../modules/nf-core/bcftools/query/main.nf' +include { BCFTOOLS_QUERY } from '../../../../../modules/nf-core/bcftools/query/main.nf' workflow test_bcftools_query { diff --git a/tests/modules/nf-core/bcftools/reheader/main.nf b/tests/modules/nf-core/bcftools/reheader/main.nf index a84eba199ba..8fdafb33429 100644 --- a/tests/modules/nf-core/bcftools/reheader/main.nf +++ b/tests/modules/nf-core/bcftools/reheader/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_REHEADER } from '../../../../modules/nf-core/bcftools/reheader/main.nf' +include { BCFTOOLS_REHEADER } from '../../../../../modules/nf-core/bcftools/reheader/main.nf' workflow test_bcftools_reheader_update_sequences { diff --git a/tests/modules/nf-core/bcftools/roh/main.nf b/tests/modules/nf-core/bcftools/roh/main.nf index b71696c78d3..d18a0aecefc 100644 --- a/tests/modules/nf-core/bcftools/roh/main.nf +++ b/tests/modules/nf-core/bcftools/roh/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_ROH } from '../../../../modules/nf-core/bcftools/roh/main.nf' +include { BCFTOOLS_ROH } from '../../../../../modules/nf-core/bcftools/roh/main.nf' workflow test_bcftools_roh { diff --git a/tests/modules/nf-core/bcftools/sort/main.nf b/tests/modules/nf-core/bcftools/sort/main.nf index e649bb3d52f..d4960fccd97 100644 --- a/tests/modules/nf-core/bcftools/sort/main.nf +++ b/tests/modules/nf-core/bcftools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_SORT } from '../../../../modules/nf-core/bcftools/sort/main.nf' +include { BCFTOOLS_SORT } from '../../../../../modules/nf-core/bcftools/sort/main.nf' workflow test_bcftools_sort { diff --git a/tests/modules/nf-core/bcftools/stats/main.nf b/tests/modules/nf-core/bcftools/stats/main.nf index 59064e11851..c8ceb924c2d 100644 --- a/tests/modules/nf-core/bcftools/stats/main.nf +++ b/tests/modules/nf-core/bcftools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_STATS } from '../../../../modules/nf-core/bcftools/stats/main.nf' +include { BCFTOOLS_STATS } from '../../../../../modules/nf-core/bcftools/stats/main.nf' workflow test_bcftools_stats { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/bcftools/view/main.nf b/tests/modules/nf-core/bcftools/view/main.nf index 43aa7d64895..d06a242111f 100644 --- a/tests/modules/nf-core/bcftools/view/main.nf +++ b/tests/modules/nf-core/bcftools/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_VIEW } from '../../../../modules/nf-core/bcftools/view/main.nf' +include { BCFTOOLS_VIEW } from '../../../../../modules/nf-core/bcftools/view/main.nf' workflow test_bcftools_view { diff --git a/tests/modules/nf-core/bcl2fastq/main.nf b/tests/modules/nf-core/bcl2fastq/main.nf index 18ad2ef1a84..9718f573257 100644 --- a/tests/modules/nf-core/bcl2fastq/main.nf +++ b/tests/modules/nf-core/bcl2fastq/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCL2FASTQ } from '../../../modules/nf-core/bcl2fastq/main.nf' -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { BCL2FASTQ } from '../../../../modules/nf-core/bcl2fastq/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_bcl2fastq { ch_flowcell = Channel.value([ diff --git a/tests/modules/nf-core/bclconvert/main.nf b/tests/modules/nf-core/bclconvert/main.nf index aaba14bd5c1..74640d5a4d6 100644 --- a/tests/modules/nf-core/bclconvert/main.nf +++ b/tests/modules/nf-core/bclconvert/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BCLCONVERT } from '../../../modules/nf-core/bclconvert/main.nf' -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { BCLCONVERT } from '../../../../modules/nf-core/bclconvert/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_bclconvert { ch_flowcell = Channel.value([ diff --git a/tests/modules/nf-core/bedtools/bamtobed/main.nf b/tests/modules/nf-core/bedtools/bamtobed/main.nf index 95aa07d21e7..26db37effa9 100644 --- a/tests/modules/nf-core/bedtools/bamtobed/main.nf +++ b/tests/modules/nf-core/bedtools/bamtobed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_BAMTOBED } from '../../../../modules/nf-core/bedtools/bamtobed/main.nf' +include { BEDTOOLS_BAMTOBED } from '../../../../../modules/nf-core/bedtools/bamtobed/main.nf' workflow test_bedtools_bamtobed { input = [ [ id:'test'], //meta map diff --git a/tests/modules/nf-core/bedtools/complement/main.nf b/tests/modules/nf-core/bedtools/complement/main.nf index 01aa5e7867e..e379ee4761d 100644 --- a/tests/modules/nf-core/bedtools/complement/main.nf +++ b/tests/modules/nf-core/bedtools/complement/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_COMPLEMENT } from '../../../../modules/nf-core/bedtools/complement/main.nf' +include { BEDTOOLS_COMPLEMENT } from '../../../../../modules/nf-core/bedtools/complement/main.nf' workflow test_bedtools_complement { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/genomecov/main.nf b/tests/modules/nf-core/bedtools/genomecov/main.nf index 1d151ddfb7f..c808b1a4b47 100644 --- a/tests/modules/nf-core/bedtools/genomecov/main.nf +++ b/tests/modules/nf-core/bedtools/genomecov/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_GENOMECOV } from '../../../../modules/nf-core/bedtools/genomecov/main.nf' +include { BEDTOOLS_GENOMECOV } from '../../../../../modules/nf-core/bedtools/genomecov/main.nf' workflow test_bedtools_genomecov_noscale { input = [ diff --git a/tests/modules/nf-core/bedtools/getfasta/main.nf b/tests/modules/nf-core/bedtools/getfasta/main.nf index a5f018ba3d8..664346cb3da 100644 --- a/tests/modules/nf-core/bedtools/getfasta/main.nf +++ b/tests/modules/nf-core/bedtools/getfasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_GETFASTA } from '../../../../modules/nf-core/bedtools/getfasta/main.nf' +include { BEDTOOLS_GETFASTA } from '../../../../../modules/nf-core/bedtools/getfasta/main.nf' workflow test_bedtools_getfasta { bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) diff --git a/tests/modules/nf-core/bedtools/intersect/main.nf b/tests/modules/nf-core/bedtools/intersect/main.nf index 69dfd6e1788..cdee9a3c1f7 100644 --- a/tests/modules/nf-core/bedtools/intersect/main.nf +++ b/tests/modules/nf-core/bedtools/intersect/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_INTERSECT } from '../../../../modules/nf-core/bedtools/intersect/main.nf' +include { BEDTOOLS_INTERSECT } from '../../../../../modules/nf-core/bedtools/intersect/main.nf' workflow test_bedtools_intersect { input = [ diff --git a/tests/modules/nf-core/bedtools/makewindows/main.nf b/tests/modules/nf-core/bedtools/makewindows/main.nf index e42a02b51ec..8928a772b43 100644 --- a/tests/modules/nf-core/bedtools/makewindows/main.nf +++ b/tests/modules/nf-core/bedtools/makewindows/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/nf-core/bedtools/makewindows/main.nf' +include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf' workflow test_bedtools_makewindows { diff --git a/tests/modules/nf-core/bedtools/maskfasta/main.nf b/tests/modules/nf-core/bedtools/maskfasta/main.nf index 634d9b76fa3..115a44e6b6e 100644 --- a/tests/modules/nf-core/bedtools/maskfasta/main.nf +++ b/tests/modules/nf-core/bedtools/maskfasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_MASKFASTA } from '../../../../modules/nf-core/bedtools/maskfasta/main.nf' +include { BEDTOOLS_MASKFASTA } from '../../../../../modules/nf-core/bedtools/maskfasta/main.nf' workflow test_bedtools_maskfasta { bed = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/merge/main.nf b/tests/modules/nf-core/bedtools/merge/main.nf index 6f5ea5e4a13..a1a84527fd3 100644 --- a/tests/modules/nf-core/bedtools/merge/main.nf +++ b/tests/modules/nf-core/bedtools/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_MERGE } from '../../../../modules/nf-core/bedtools/merge/main.nf' +include { BEDTOOLS_MERGE } from '../../../../../modules/nf-core/bedtools/merge/main.nf' workflow test_bedtools_merge { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/slop/main.nf b/tests/modules/nf-core/bedtools/slop/main.nf index 413f420e7d9..40531695034 100644 --- a/tests/modules/nf-core/bedtools/slop/main.nf +++ b/tests/modules/nf-core/bedtools/slop/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SLOP } from '../../../../modules/nf-core/bedtools/slop/main.nf' +include { BEDTOOLS_SLOP } from '../../../../../modules/nf-core/bedtools/slop/main.nf' workflow test_bedtools_slop { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/sort/main.nf b/tests/modules/nf-core/bedtools/sort/main.nf index d35365700e7..b7652a88a07 100644 --- a/tests/modules/nf-core/bedtools/sort/main.nf +++ b/tests/modules/nf-core/bedtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SORT } from '../../../../modules/nf-core/bedtools/sort/main.nf' +include { BEDTOOLS_SORT } from '../../../../../modules/nf-core/bedtools/sort/main.nf' workflow test_bedtools_sort { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/bedtools/split/main.nf b/tests/modules/nf-core/bedtools/split/main.nf index 925606bcae6..f4818503a3d 100644 --- a/tests/modules/nf-core/bedtools/split/main.nf +++ b/tests/modules/nf-core/bedtools/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SPLIT } from '../../../../modules/nf-core/bedtools/split/main.nf' +include { BEDTOOLS_SPLIT } from '../../../../../modules/nf-core/bedtools/split/main.nf' workflow test_bedtools_split { diff --git a/tests/modules/nf-core/bedtools/subtract/main.nf b/tests/modules/nf-core/bedtools/subtract/main.nf index 92056f506e4..a86c81a1870 100644 --- a/tests/modules/nf-core/bedtools/subtract/main.nf +++ b/tests/modules/nf-core/bedtools/subtract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BEDTOOLS_SUBTRACT } from '../../../../modules/nf-core/bedtools/subtract/main.nf' +include { BEDTOOLS_SUBTRACT } from '../../../../../modules/nf-core/bedtools/subtract/main.nf' workflow test_bedtools_subtract { input = [ diff --git a/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf b/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf index 8c3666605a6..2f349907adf 100644 --- a/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf +++ b/tests/modules/nf-core/biobambam/bammarkduplicates2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../modules/nf-core/biobambam/bammarkduplicates2/main.nf' +include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../../modules/nf-core/biobambam/bammarkduplicates2/main.nf' workflow test_biobambam_bammarkduplicates2 { diff --git a/tests/modules/nf-core/biobambam/bammerge/main.nf b/tests/modules/nf-core/biobambam/bammerge/main.nf index 003c570ce32..8c92c7dba70 100644 --- a/tests/modules/nf-core/biobambam/bammerge/main.nf +++ b/tests/modules/nf-core/biobambam/bammerge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BIOBAMBAM_BAMMERGE } from '../../../../modules/nf-core/biobambam/bammerge/main.nf' +include { BIOBAMBAM_BAMMERGE } from '../../../../../modules/nf-core/biobambam/bammerge/main.nf' workflow test_biobambam_bammerge_paired { diff --git a/tests/modules/nf-core/biobambam/bamsormadup/main.nf b/tests/modules/nf-core/biobambam/bamsormadup/main.nf index 3afcf9a8438..1f9adae5ac5 100644 --- a/tests/modules/nf-core/biobambam/bamsormadup/main.nf +++ b/tests/modules/nf-core/biobambam/bamsormadup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/nf-core/biobambam/bamsormadup/main.nf' +include { BIOBAMBAM_BAMSORMADUP } from '../../../../../modules/nf-core/biobambam/bamsormadup/main.nf' workflow test_biobambam_bamsormadup_multi_input { diff --git a/tests/modules/nf-core/biscuit/align/main.nf b/tests/modules/nf-core/biscuit/align/main.nf index 7e3c91a3a74..00fe14d6bb8 100644 --- a/tests/modules/nf-core/biscuit/align/main.nf +++ b/tests/modules/nf-core/biscuit/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../modules/nf-core/biscuit/align/main.nf' -include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../modules/nf-core/biscuit/align/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../../modules/nf-core/biscuit/align/main.nf' +include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../../modules/nf-core/biscuit/align/main.nf' // Single-end test diff --git a/tests/modules/nf-core/biscuit/biscuitblaster/main.nf b/tests/modules/nf-core/biscuit/biscuitblaster/main.nf index fe15d373732..7db9d4c528d 100644 --- a/tests/modules/nf-core/biscuit/biscuitblaster/main.nf +++ b/tests/modules/nf-core/biscuit/biscuitblaster/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../modules/nf-core/biscuit/biscuitblaster/main.nf' -include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../modules/nf-core/biscuit/biscuitblaster/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../../modules/nf-core/biscuit/biscuitblaster/main.nf' +include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../../modules/nf-core/biscuit/biscuitblaster/main.nf' // Single-end test workflow test_biscuit_blaster_single { diff --git a/tests/modules/nf-core/biscuit/bsconv/main.nf b/tests/modules/nf-core/biscuit/bsconv/main.nf index 0de88274a9f..14bc0e22439 100644 --- a/tests/modules/nf-core/biscuit/bsconv/main.nf +++ b/tests/modules/nf-core/biscuit/bsconv/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_BSCONV } from '../../../../modules/nf-core/biscuit/bsconv/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_BSCONV } from '../../../../../modules/nf-core/biscuit/bsconv/main.nf' workflow test_biscuit_bsconv { diff --git a/tests/modules/nf-core/biscuit/epiread/main.nf b/tests/modules/nf-core/biscuit/epiread/main.nf index 243744edc1a..13eb7afce98 100644 --- a/tests/modules/nf-core/biscuit/epiread/main.nf +++ b/tests/modules/nf-core/biscuit/epiread/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_EPIREAD } from '../../../../modules/nf-core/biscuit/epiread/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_EPIREAD } from '../../../../../modules/nf-core/biscuit/epiread/main.nf' workflow test_biscuit_epiread_nosnp { diff --git a/tests/modules/nf-core/biscuit/index/main.nf b/tests/modules/nf-core/biscuit/index/main.nf index 8d4cfd857cf..6ac491306f9 100644 --- a/tests/modules/nf-core/biscuit/index/main.nf +++ b/tests/modules/nf-core/biscuit/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' workflow test_biscuit_index { diff --git a/tests/modules/nf-core/biscuit/mergecg/main.nf b/tests/modules/nf-core/biscuit/mergecg/main.nf index edb36d46183..9eade987eaa 100644 --- a/tests/modules/nf-core/biscuit/mergecg/main.nf +++ b/tests/modules/nf-core/biscuit/mergecg/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_MERGECG } from '../../../../modules/nf-core/biscuit/mergecg/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_MERGECG } from '../../../../../modules/nf-core/biscuit/mergecg/main.nf' workflow test_biscuit_mergecg { diff --git a/tests/modules/nf-core/biscuit/pileup/main.nf b/tests/modules/nf-core/biscuit/pileup/main.nf index 74b1eb26f56..7f9ebb4fb07 100644 --- a/tests/modules/nf-core/biscuit/pileup/main.nf +++ b/tests/modules/nf-core/biscuit/pileup/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_PILEUP } from '../../../../modules/nf-core/biscuit/pileup/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_PILEUP } from '../../../../../modules/nf-core/biscuit/pileup/main.nf' workflow test_biscuit_pileup { diff --git a/tests/modules/nf-core/biscuit/qc/main.nf b/tests/modules/nf-core/biscuit/qc/main.nf index 5752b19f3f3..8f226b1d774 100644 --- a/tests/modules/nf-core/biscuit/qc/main.nf +++ b/tests/modules/nf-core/biscuit/qc/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISCUIT_INDEX } from '../../../../modules/nf-core/biscuit/index/main.nf' -include { BISCUIT_QC } from '../../../../modules/nf-core/biscuit/qc/main.nf' +include { BISCUIT_INDEX } from '../../../../../modules/nf-core/biscuit/index/main.nf' +include { BISCUIT_QC } from '../../../../../modules/nf-core/biscuit/qc/main.nf' workflow test_biscuit_qc { diff --git a/tests/modules/nf-core/biscuit/vcf2bed/main.nf b/tests/modules/nf-core/biscuit/vcf2bed/main.nf index a69ff548782..3f9828080f1 100644 --- a/tests/modules/nf-core/biscuit/vcf2bed/main.nf +++ b/tests/modules/nf-core/biscuit/vcf2bed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISCUIT_VCF2BED } from '../../../../modules/nf-core/biscuit/vcf2bed/main.nf' +include { BISCUIT_VCF2BED } from '../../../../../modules/nf-core/biscuit/vcf2bed/main.nf' workflow test_biscuit_vcf2bed { diff --git a/tests/modules/nf-core/bismark/align/main.nf b/tests/modules/nf-core/bismark/align/main.nf index 6823b581a0e..c24e751c919 100644 --- a/tests/modules/nf-core/bismark/align/main.nf +++ b/tests/modules/nf-core/bismark/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' -include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../modules/nf-core/bismark/align/main.nf' -include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../../modules/nf-core/bismark/align/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bismark/deduplicate/main.nf b/tests/modules/nf-core/bismark/deduplicate/main.nf index 0e90444361d..7f1ae9c127b 100644 --- a/tests/modules/nf-core/bismark/deduplicate/main.nf +++ b/tests/modules/nf-core/bismark/deduplicate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISMARK_DEDUPLICATE } from '../../../../modules/nf-core/bismark/deduplicate/main.nf' +include { BISMARK_DEDUPLICATE } from '../../../../../modules/nf-core/bismark/deduplicate/main.nf' workflow test_bismark_deduplicate { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/bismark/genomepreparation/main.nf b/tests/modules/nf-core/bismark/genomepreparation/main.nf index 60a69ff47e4..71b77805193 100644 --- a/tests/modules/nf-core/bismark/genomepreparation/main.nf +++ b/tests/modules/nf-core/bismark/genomepreparation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf' workflow test_bismark_genomepreparation { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bismark/methylationextractor/main.nf b/tests/modules/nf-core/bismark/methylationextractor/main.nf index 7b529bb8dad..6c11f013bc4 100644 --- a/tests/modules/nf-core/bismark/methylationextractor/main.nf +++ b/tests/modules/nf-core/bismark/methylationextractor/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/nf-core/bismark/methylationextractor/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../../modules/nf-core/bismark/methylationextractor/main.nf' workflow test_bismark_methylationextractor { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/bismark/report/main.nf b/tests/modules/nf-core/bismark/report/main.nf index 6451ae684c7..df1567c43a2 100644 --- a/tests/modules/nf-core/bismark/report/main.nf +++ b/tests/modules/nf-core/bismark/report/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' -include { BISMARK_ALIGN } from '../../../../modules/nf-core/bismark/align/main.nf' -include { BISMARK_DEDUPLICATE } from '../../../../modules/nf-core/bismark/deduplicate/main.nf' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/nf-core/bismark/methylationextractor/main.nf' -include { BISMARK_REPORT } from '../../../../modules/nf-core/bismark/report/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_ALIGN } from '../../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_DEDUPLICATE } from '../../../../../modules/nf-core/bismark/deduplicate/main.nf' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../../modules/nf-core/bismark/methylationextractor/main.nf' +include { BISMARK_REPORT } from '../../../../../modules/nf-core/bismark/report/main.nf' workflow test_bismark_report { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/bismark/summary/main.nf b/tests/modules/nf-core/bismark/summary/main.nf index e1b78ff7464..89bb91a0162 100644 --- a/tests/modules/nf-core/bismark/summary/main.nf +++ b/tests/modules/nf-core/bismark/summary/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { BISMARK_GENOMEPREPARATION } from '../../../../modules/nf-core/bismark/genomepreparation/main.nf' -include { BISMARK_ALIGN } from '../../../../modules/nf-core/bismark/align/main.nf' -include { BISMARK_DEDUPLICATE } from '../../../../modules/nf-core/bismark/deduplicate/main.nf' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/nf-core/bismark/methylationextractor/main.nf' -include { BISMARK_SUMMARY } from '../../../../modules/nf-core/bismark/summary/main.nf' +include { BISMARK_GENOMEPREPARATION } from '../../../../../modules/nf-core/bismark/genomepreparation/main.nf' +include { BISMARK_ALIGN } from '../../../../../modules/nf-core/bismark/align/main.nf' +include { BISMARK_DEDUPLICATE } from '../../../../../modules/nf-core/bismark/deduplicate/main.nf' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../../modules/nf-core/bismark/methylationextractor/main.nf' +include { BISMARK_SUMMARY } from '../../../../../modules/nf-core/bismark/summary/main.nf' workflow test_bismark_summary { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/blast/blastn/main.nf b/tests/modules/nf-core/blast/blastn/main.nf index 074cb6a3162..cb0f8bdf52c 100644 --- a/tests/modules/nf-core/blast/blastn/main.nf +++ b/tests/modules/nf-core/blast/blastn/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BLAST_MAKEBLASTDB } from '../../../../modules/nf-core/blast/makeblastdb/main.nf' -include { BLAST_BLASTN } from '../../../../modules/nf-core/blast/blastn/main.nf' +include { BLAST_MAKEBLASTDB } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf' +include { BLAST_BLASTN } from '../../../../../modules/nf-core/blast/blastn/main.nf' workflow test_blast_blastn { input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/blast/makeblastdb/main.nf b/tests/modules/nf-core/blast/makeblastdb/main.nf index f8fb262c1eb..6822a9fb4ab 100644 --- a/tests/modules/nf-core/blast/makeblastdb/main.nf +++ b/tests/modules/nf-core/blast/makeblastdb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BLAST_MAKEBLASTDB } from '../../../../modules/nf-core/blast/makeblastdb/main.nf' +include { BLAST_MAKEBLASTDB } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf' workflow test_blast_makeblastdb { input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/blast/tblastn/main.nf b/tests/modules/nf-core/blast/tblastn/main.nf index 7fd65f94293..ee40d8386f0 100644 --- a/tests/modules/nf-core/blast/tblastn/main.nf +++ b/tests/modules/nf-core/blast/tblastn/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BLAST_TBLASTN } from '../../../../modules/nf-core/blast/tblastn/main.nf' -include { BLAST_MAKEBLASTDB } from '../../../../modules/nf-core/blast/makeblastdb/main.nf' +include { BLAST_TBLASTN } from '../../../../../modules/nf-core/blast/tblastn/main.nf' +include { BLAST_MAKEBLASTDB } from '../../../../../modules/nf-core/blast/makeblastdb/main.nf' workflow test_blast_tblastn { diff --git a/tests/modules/nf-core/bowtie/align/main.nf b/tests/modules/nf-core/bowtie/align/main.nf index 85a58d019ea..96863814855 100644 --- a/tests/modules/nf-core/bowtie/align/main.nf +++ b/tests/modules/nf-core/bowtie/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BOWTIE_BUILD } from '../../../../modules/nf-core/bowtie/build/main.nf' -include { BOWTIE_ALIGN } from '../../../../modules/nf-core/bowtie/align/main.nf' +include { BOWTIE_BUILD } from '../../../../../modules/nf-core/bowtie/build/main.nf' +include { BOWTIE_ALIGN } from '../../../../../modules/nf-core/bowtie/align/main.nf' workflow test_bowtie_align_single_end { input = [ diff --git a/tests/modules/nf-core/bowtie/build_test/main.nf b/tests/modules/nf-core/bowtie/build_test/main.nf index eb0c3dd930f..23356ec35f5 100644 --- a/tests/modules/nf-core/bowtie/build_test/main.nf +++ b/tests/modules/nf-core/bowtie/build_test/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE_BUILD } from '../../../../modules/nf-core/bowtie/build/main.nf' +include { BOWTIE_BUILD } from '../../../../../modules/nf-core/bowtie/build/main.nf' workflow test_bowtie_build { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bowtie2/align/main.nf b/tests/modules/nf-core/bowtie2/align/main.nf index 0645d198a63..40f46b227b6 100644 --- a/tests/modules/nf-core/bowtie2/align/main.nf +++ b/tests/modules/nf-core/bowtie2/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../../modules/nf-core/bowtie2/build/main.nf' -include { BOWTIE2_ALIGN } from '../../../../modules/nf-core/bowtie2/align/main.nf' +include { BOWTIE2_BUILD } from '../../../../../modules/nf-core/bowtie2/build/main.nf' +include { BOWTIE2_ALIGN } from '../../../../../modules/nf-core/bowtie2/align/main.nf' workflow test_bowtie2_align_single_end { input = [ diff --git a/tests/modules/nf-core/bowtie2/build_test/main.nf b/tests/modules/nf-core/bowtie2/build_test/main.nf index c2042c0fd1c..350010dd619 100644 --- a/tests/modules/nf-core/bowtie2/build_test/main.nf +++ b/tests/modules/nf-core/bowtie2/build_test/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BOWTIE2_BUILD } from '../../../../modules/nf-core/bowtie2/build/main.nf' +include { BOWTIE2_BUILD } from '../../../../../modules/nf-core/bowtie2/build/main.nf' workflow test_bowtie2_build { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bracken/bracken/main.nf b/tests/modules/nf-core/bracken/bracken/main.nf index fda8efab40b..abd4b62cc53 100644 --- a/tests/modules/nf-core/bracken/bracken/main.nf +++ b/tests/modules/nf-core/bracken/bracken/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main.nf' -include { BRACKEN_BRACKEN } from '../../../../modules/nf-core/bracken/bracken/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main.nf' +include { BRACKEN_BRACKEN } from '../../../../../modules/nf-core/bracken/bracken/main.nf' workflow test_bracken_bracken_single_end_default_args { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf b/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf index aea65aebbbe..333156d4d8f 100644 --- a/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf +++ b/tests/modules/nf-core/bracken/combinebrackenoutputs/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main.nf' -include { BRACKEN_BRACKEN } from '../../../../modules/nf-core/bracken/bracken/main.nf' -include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/nf-core/bracken/combinebrackenoutputs/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main.nf' +include { BRACKEN_BRACKEN } from '../../../../../modules/nf-core/bracken/bracken/main.nf' +include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../../modules/nf-core/bracken/combinebrackenoutputs/main.nf' workflow test_bracken_combinebrackenoutputs { diff --git a/tests/modules/nf-core/busco/main.nf b/tests/modules/nf-core/busco/main.nf index 30176d486a3..6618b589af2 100644 --- a/tests/modules/nf-core/busco/main.nf +++ b/tests/modules/nf-core/busco/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BUSCO } from '../../../modules/nf-core/busco/main.nf' +include { BUSCO } from '../../../../modules/nf-core/busco/main.nf' workflow test_busco_genome_single_fasta { diff --git a/tests/modules/nf-core/bwa/aln/main.nf b/tests/modules/nf-core/bwa/aln/main.nf index 92d899f4648..0b5458d66b4 100644 --- a/tests/modules/nf-core/bwa/aln/main.nf +++ b/tests/modules/nf-core/bwa/aln/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' -include { BWA_ALN } from '../../../../modules/nf-core/bwa/aln/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_ALN } from '../../../../../modules/nf-core/bwa/aln/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwa/index/main.nf b/tests/modules/nf-core/bwa/index/main.nf index 4426f94066b..956ba083c91 100644 --- a/tests/modules/nf-core/bwa/index/main.nf +++ b/tests/modules/nf-core/bwa/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' workflow test_bwa_index { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bwa/mem/main.nf b/tests/modules/nf-core/bwa/mem/main.nf index 34e6a6732c6..2378144581a 100644 --- a/tests/modules/nf-core/bwa/mem/main.nf +++ b/tests/modules/nf-core/bwa/mem/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' -include { BWA_MEM } from '../../../../modules/nf-core/bwa/mem/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM } from '../../../../../modules/nf-core/bwa/mem/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwa/sampe/main.nf b/tests/modules/nf-core/bwa/sampe/main.nf index e57a26ae104..a250d5a9664 100644 --- a/tests/modules/nf-core/bwa/sampe/main.nf +++ b/tests/modules/nf-core/bwa/sampe/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' -include { BWA_ALN } from '../../../../modules/nf-core/bwa/aln/main.nf' -include { BWA_SAMPE } from '../../../../modules/nf-core/bwa/sampe/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_ALN } from '../../../../../modules/nf-core/bwa/aln/main.nf' +include { BWA_SAMPE } from '../../../../../modules/nf-core/bwa/sampe/main.nf' workflow test_bwa_sampe { diff --git a/tests/modules/nf-core/bwa/samse/main.nf b/tests/modules/nf-core/bwa/samse/main.nf index 283fed3e63c..b8cc2e2b5e1 100644 --- a/tests/modules/nf-core/bwa/samse/main.nf +++ b/tests/modules/nf-core/bwa/samse/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' -include { BWA_ALN } from '../../../../modules/nf-core/bwa/aln/main.nf' -include { BWA_SAMSE } from '../../../../modules/nf-core/bwa/samse/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_ALN } from '../../../../../modules/nf-core/bwa/aln/main.nf' +include { BWA_SAMSE } from '../../../../../modules/nf-core/bwa/samse/main.nf' workflow test_bwa_samse { diff --git a/tests/modules/nf-core/bwamem2/index/main.nf b/tests/modules/nf-core/bwamem2/index/main.nf index 79706edeb1b..c4c16298aa0 100644 --- a/tests/modules/nf-core/bwamem2/index/main.nf +++ b/tests/modules/nf-core/bwamem2/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWAMEM2_INDEX } from '../../../../modules/nf-core/bwamem2/index/main.nf' +include { BWAMEM2_INDEX } from '../../../../../modules/nf-core/bwamem2/index/main.nf' workflow test_bwamem2_index { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/bwamem2/mem/main.nf b/tests/modules/nf-core/bwamem2/mem/main.nf index 39159a454bf..e53446a845d 100644 --- a/tests/modules/nf-core/bwamem2/mem/main.nf +++ b/tests/modules/nf-core/bwamem2/mem/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWAMEM2_INDEX } from '../../../../modules/nf-core/bwamem2/index/main.nf' -include { BWAMEM2_MEM } from '../../../../modules/nf-core/bwamem2/mem/main.nf' +include { BWAMEM2_INDEX } from '../../../../../modules/nf-core/bwamem2/index/main.nf' +include { BWAMEM2_MEM } from '../../../../../modules/nf-core/bwamem2/mem/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwameth/align/main.nf b/tests/modules/nf-core/bwameth/align/main.nf index 0c1a7db70a6..5128ab8bdf3 100644 --- a/tests/modules/nf-core/bwameth/align/main.nf +++ b/tests/modules/nf-core/bwameth/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { BWAMETH_INDEX } from '../../../../modules/nf-core/bwameth/index/main.nf' -include { BWAMETH_ALIGN } from '../../../../modules/nf-core/bwameth/align/main.nf' +include { BWAMETH_INDEX } from '../../../../../modules/nf-core/bwameth/index/main.nf' +include { BWAMETH_ALIGN } from '../../../../../modules/nf-core/bwameth/align/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/bwameth/index/main.nf b/tests/modules/nf-core/bwameth/index/main.nf index b65969b745d..14f27490bb2 100644 --- a/tests/modules/nf-core/bwameth/index/main.nf +++ b/tests/modules/nf-core/bwameth/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BWAMETH_INDEX } from '../../../../modules/nf-core/bwameth/index/main.nf' +include { BWAMETH_INDEX } from '../../../../../modules/nf-core/bwameth/index/main.nf' workflow test_bwameth_index { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/cat/cat/main.nf b/tests/modules/nf-core/cat/cat/main.nf index ff12494b3c4..da8823c2c63 100644 --- a/tests/modules/nf-core/cat/cat/main.nf +++ b/tests/modules/nf-core/cat/cat/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CAT_CAT } from '../../../../modules/nf-core/cat/cat/main.nf' -include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/nf-core/cat/cat/main.nf' -include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/nf-core/cat/cat/main.nf' +include { CAT_CAT } from '../../../../../modules/nf-core/cat/cat/main.nf' +include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../../modules/nf-core/cat/cat/main.nf' +include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../../modules/nf-core/cat/cat/main.nf' workflow test_cat_unzipped_unzipped { diff --git a/tests/modules/nf-core/cat/fastq/main.nf b/tests/modules/nf-core/cat/fastq/main.nf index 1e0037968db..dbd61f8441e 100644 --- a/tests/modules/nf-core/cat/fastq/main.nf +++ b/tests/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CAT_FASTQ } from '../../../../modules/nf-core/cat/fastq/main.nf' +include { CAT_FASTQ } from '../../../../../modules/nf-core/cat/fastq/main.nf' workflow test_cat_fastq_single_end { input = [ diff --git a/tests/modules/nf-core/cellranger/count/main.nf b/tests/modules/nf-core/cellranger/count/main.nf index 1e1133af50b..f4746db4bfd 100644 --- a/tests/modules/nf-core/cellranger/count/main.nf +++ b/tests/modules/nf-core/cellranger/count/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CELLRANGER_MKGTF } from '../../../../modules/nf-core/cellranger/mkgtf/main.nf' -include { CELLRANGER_MKREF } from '../../../../modules/nf-core/cellranger/mkref/main.nf' -include { CELLRANGER_COUNT } from '../../../../modules/nf-core/cellranger/count/main.nf' +include { CELLRANGER_MKGTF } from '../../../../../modules/nf-core/cellranger/mkgtf/main.nf' +include { CELLRANGER_MKREF } from '../../../../../modules/nf-core/cellranger/mkref/main.nf' +include { CELLRANGER_COUNT } from '../../../../../modules/nf-core/cellranger/count/main.nf' workflow test_cellranger_count { diff --git a/tests/modules/nf-core/cellranger/mkfastq/main.nf b/tests/modules/nf-core/cellranger/mkfastq/main.nf index 486b33cc428..80434d5d5e8 100644 --- a/tests/modules/nf-core/cellranger/mkfastq/main.nf +++ b/tests/modules/nf-core/cellranger/mkfastq/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { CELLRANGER_MKFASTQ } from '../../../../modules/nf-core/cellranger/mkfastq/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { CELLRANGER_MKFASTQ } from '../../../../../modules/nf-core/cellranger/mkfastq/main.nf' workflow test_cellranger_mkfastq_simple { diff --git a/tests/modules/nf-core/cellranger/mkgtf/main.nf b/tests/modules/nf-core/cellranger/mkgtf/main.nf index 7dad0e3147a..cb281beee37 100644 --- a/tests/modules/nf-core/cellranger/mkgtf/main.nf +++ b/tests/modules/nf-core/cellranger/mkgtf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CELLRANGER_MKGTF } from '../../../../modules/nf-core/cellranger/mkgtf/main.nf' +include { CELLRANGER_MKGTF } from '../../../../../modules/nf-core/cellranger/mkgtf/main.nf' workflow test_cellranger_mkgtf { gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) diff --git a/tests/modules/nf-core/cellranger/mkref/main.nf b/tests/modules/nf-core/cellranger/mkref/main.nf index 7063715ae04..05f85805a01 100644 --- a/tests/modules/nf-core/cellranger/mkref/main.nf +++ b/tests/modules/nf-core/cellranger/mkref/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CELLRANGER_MKREF } from '../../../../modules/nf-core/cellranger/mkref/main.nf' +include { CELLRANGER_MKREF } from '../../../../../modules/nf-core/cellranger/mkref/main.nf' workflow test_cellranger_mkref { diff --git a/tests/modules/nf-core/centrifuge/centrifuge/main.nf b/tests/modules/nf-core/centrifuge/centrifuge/main.nf index 860378b31a2..ab91d9f001e 100644 --- a/tests/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/tests/modules/nf-core/centrifuge/centrifuge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/nf-core/centrifuge/centrifuge/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { CENTRIFUGE_CENTRIFUGE } from '../../../../../modules/nf-core/centrifuge/centrifuge/main.nf' workflow test_centrifuge_centrifuge_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/centrifuge/kreport/main.nf b/tests/modules/nf-core/centrifuge/kreport/main.nf index f7e3c29b7f2..517b72a5aec 100644 --- a/tests/modules/nf-core/centrifuge/kreport/main.nf +++ b/tests/modules/nf-core/centrifuge/kreport/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/nf-core/centrifuge/centrifuge/main.nf' -include { CENTRIFUGE_KREPORT } from '../../../../modules/nf-core/centrifuge/kreport/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { CENTRIFUGE_CENTRIFUGE } from '../../../../../modules/nf-core/centrifuge/centrifuge/main.nf' +include { CENTRIFUGE_KREPORT } from '../../../../../modules/nf-core/centrifuge/kreport/main.nf' workflow test_centrifuge_kreport_single_end { diff --git a/tests/modules/nf-core/checkm/lineagewf/main.nf b/tests/modules/nf-core/checkm/lineagewf/main.nf index 53fb44efe2e..eb7bedd8110 100644 --- a/tests/modules/nf-core/checkm/lineagewf/main.nf +++ b/tests/modules/nf-core/checkm/lineagewf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CHECKM_LINEAGEWF } from '../../../../modules/nf-core/checkm/lineagewf/main.nf' +include { CHECKM_LINEAGEWF } from '../../../../../modules/nf-core/checkm/lineagewf/main.nf' workflow test_checkm_lineagewf { diff --git a/tests/modules/nf-core/checkm/qa/main.nf b/tests/modules/nf-core/checkm/qa/main.nf index 035d9cda56b..8f4c64e5630 100644 --- a/tests/modules/nf-core/checkm/qa/main.nf +++ b/tests/modules/nf-core/checkm/qa/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { CHECKM_LINEAGEWF } from '../../../../modules/nf-core/checkm/lineagewf/main.nf' -include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA } from '../../../../modules/nf-core/checkm/lineagewf/main.nf' -include { CHECKM_QA } from '../../../../modules/nf-core/checkm/qa/main.nf' -include { CHECKM_QA as CHECKM_QA_FASTA } from '../../../../modules/nf-core/checkm/qa/main.nf' +include { CHECKM_LINEAGEWF } from '../../../../../modules/nf-core/checkm/lineagewf/main.nf' +include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA } from '../../../../../modules/nf-core/checkm/lineagewf/main.nf' +include { CHECKM_QA } from '../../../../../modules/nf-core/checkm/qa/main.nf' +include { CHECKM_QA as CHECKM_QA_FASTA } from '../../../../../modules/nf-core/checkm/qa/main.nf' workflow test_checkm_qa { diff --git a/tests/modules/nf-core/chromap/chromap/main.nf b/tests/modules/nf-core/chromap/chromap/main.nf index 30d73410eee..97f5f737ed6 100644 --- a/tests/modules/nf-core/chromap/chromap/main.nf +++ b/tests/modules/nf-core/chromap/chromap/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CHROMAP_INDEX } from '../../../../modules/nf-core/chromap/index/main.nf' -include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/nf-core/chromap/chromap/main.nf' -include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../modules/nf-core/chromap/chromap/main.nf' +include { CHROMAP_INDEX } from '../../../../../modules/nf-core/chromap/index/main.nf' +include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../../modules/nf-core/chromap/chromap/main.nf' +include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../../modules/nf-core/chromap/chromap/main.nf' workflow test_chromap_chromap_single_end { diff --git a/tests/modules/nf-core/chromap/index/main.nf b/tests/modules/nf-core/chromap/index/main.nf index c649e12511a..11987851c56 100644 --- a/tests/modules/nf-core/chromap/index/main.nf +++ b/tests/modules/nf-core/chromap/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CHROMAP_INDEX } from '../../../../modules/nf-core/chromap/index/main.nf' +include { CHROMAP_INDEX } from '../../../../../modules/nf-core/chromap/index/main.nf' workflow test_chromap_index { diff --git a/tests/modules/nf-core/clonalframeml/main.nf b/tests/modules/nf-core/clonalframeml/main.nf index 2ee14d56a5f..fdd7d8ae911 100644 --- a/tests/modules/nf-core/clonalframeml/main.nf +++ b/tests/modules/nf-core/clonalframeml/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CLONALFRAMEML } from '../../../modules/nf-core/clonalframeml/main.nf' +include { CLONALFRAMEML } from '../../../../modules/nf-core/clonalframeml/main.nf' workflow test_clonalframeml { diff --git a/tests/modules/nf-core/cmseq/polymut/main.nf b/tests/modules/nf-core/cmseq/polymut/main.nf index b92115bd20e..c4535090ba0 100644 --- a/tests/modules/nf-core/cmseq/polymut/main.nf +++ b/tests/modules/nf-core/cmseq/polymut/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CMSEQ_POLYMUT } from '../../../../modules/nf-core/cmseq/polymut/main.nf' +include { CMSEQ_POLYMUT } from '../../../../../modules/nf-core/cmseq/polymut/main.nf' workflow test_cmseq_polymut_1 { diff --git a/tests/modules/nf-core/cnvkit/antitarget/main.nf b/tests/modules/nf-core/cnvkit/antitarget/main.nf index b4bc6c1be9d..6edce1d848d 100644 --- a/tests/modules/nf-core/cnvkit/antitarget/main.nf +++ b/tests/modules/nf-core/cnvkit/antitarget/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVKIT_ANTITARGET } from '../../../../modules/nf-core/cnvkit/antitarget/main.nf' +include { CNVKIT_ANTITARGET } from '../../../../../modules/nf-core/cnvkit/antitarget/main.nf' workflow test_cnvkit_antitarget { diff --git a/tests/modules/nf-core/cnvkit/batch/main.nf b/tests/modules/nf-core/cnvkit/batch/main.nf index 492e3585e94..c1fed0ed59e 100755 --- a/tests/modules/nf-core/cnvkit/batch/main.nf +++ b/tests/modules/nf-core/cnvkit/batch/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/nf-core/cnvkit/batch/main.nf' -include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/nf-core/cnvkit/batch/main.nf' -include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/nf-core/cnvkit/batch/main.nf' -include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../../modules/nf-core/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../../modules/nf-core/cnvkit/batch/main.nf' workflow test_cnvkit_hybrid_somatic { diff --git a/tests/modules/nf-core/cnvkit/reference/main.nf b/tests/modules/nf-core/cnvkit/reference/main.nf index 650bc8b0258..16358378e64 100644 --- a/tests/modules/nf-core/cnvkit/reference/main.nf +++ b/tests/modules/nf-core/cnvkit/reference/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVKIT_REFERENCE } from '../../../../modules/nf-core/cnvkit/reference/main.nf' +include { CNVKIT_REFERENCE } from '../../../../../modules/nf-core/cnvkit/reference/main.nf' workflow test_cnvkit_reference { diff --git a/tests/modules/nf-core/cnvpytor/callcnvs/main.nf b/tests/modules/nf-core/cnvpytor/callcnvs/main.nf index a580c637fd5..cbbd83c4040 100644 --- a/tests/modules/nf-core/cnvpytor/callcnvs/main.nf +++ b/tests/modules/nf-core/cnvpytor/callcnvs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_CALLCNVS } from '../../../../modules/nf-core/cnvpytor/callcnvs/main.nf' +include { CNVPYTOR_CALLCNVS } from '../../../../../modules/nf-core/cnvpytor/callcnvs/main.nf' workflow test_cnvpytor_callcnvs { diff --git a/tests/modules/nf-core/cnvpytor/histogram/main.nf b/tests/modules/nf-core/cnvpytor/histogram/main.nf index a50cf1974dc..12214e87653 100644 --- a/tests/modules/nf-core/cnvpytor/histogram/main.nf +++ b/tests/modules/nf-core/cnvpytor/histogram/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_HISTOGRAM } from '../../../../modules/nf-core/cnvpytor/histogram/main.nf' +include { CNVPYTOR_HISTOGRAM } from '../../../../../modules/nf-core/cnvpytor/histogram/main.nf' workflow test_cnvpytor_histogram { diff --git a/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf b/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf index 3b9e9b04a24..b2d3f5592d2 100644 --- a/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf +++ b/tests/modules/nf-core/cnvpytor/importreaddepth/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../modules/nf-core/cnvpytor/importreaddepth/main.nf' +include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../../modules/nf-core/cnvpytor/importreaddepth/main.nf' workflow test_cnvpytor_importreaddepth { diff --git a/tests/modules/nf-core/cnvpytor/partition/main.nf b/tests/modules/nf-core/cnvpytor/partition/main.nf index 7fe24522106..bd46cec0b9f 100644 --- a/tests/modules/nf-core/cnvpytor/partition/main.nf +++ b/tests/modules/nf-core/cnvpytor/partition/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_PARTITION } from '../../../../modules/nf-core/cnvpytor/partition/main.nf' +include { CNVPYTOR_PARTITION } from '../../../../../modules/nf-core/cnvpytor/partition/main.nf' workflow test_cnvpytor_partition { diff --git a/tests/modules/nf-core/cnvpytor/view/main.nf b/tests/modules/nf-core/cnvpytor/view/main.nf index 9ffdc6a074a..799234b0e55 100644 --- a/tests/modules/nf-core/cnvpytor/view/main.nf +++ b/tests/modules/nf-core/cnvpytor/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CNVPYTOR_VIEW } from '../../../../modules/nf-core/cnvpytor/view/main.nf' +include { CNVPYTOR_VIEW } from '../../../../../modules/nf-core/cnvpytor/view/main.nf' workflow test_cnvpytor_view { diff --git a/tests/modules/nf-core/controlfreec/assesssignificance/main.nf b/tests/modules/nf-core/controlfreec/assesssignificance/main.nf index c3fb2cb40e9..f1add9072d0 100644 --- a/tests/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/tests/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/nf-core/controlfreec/assesssignificance/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../../modules/nf-core/controlfreec/assesssignificance/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_assesssignificance { diff --git a/tests/modules/nf-core/controlfreec/freec/main.nf b/tests/modules/nf-core/controlfreec/freec/main.nf index b7c01a2dd46..3b9af3f5318 100644 --- a/tests/modules/nf-core/controlfreec/freec/main.nf +++ b/tests/modules/nf-core/controlfreec/freec/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_freec { diff --git a/tests/modules/nf-core/controlfreec/freec2bed/main.nf b/tests/modules/nf-core/controlfreec/freec2bed/main.nf index f0e0d41fd8f..16ae2a89759 100644 --- a/tests/modules/nf-core/controlfreec/freec2bed/main.nf +++ b/tests/modules/nf-core/controlfreec/freec2bed/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_FREEC2BED } from '../../../../modules/nf-core/controlfreec/freec2bed/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CONTROLFREEC_FREEC2BED } from '../../../../../modules/nf-core/controlfreec/freec2bed/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_freec2bed { diff --git a/tests/modules/nf-core/controlfreec/freec2circos/main.nf b/tests/modules/nf-core/controlfreec/freec2circos/main.nf index 32cfda5f2ec..2de1cb8fc1a 100644 --- a/tests/modules/nf-core/controlfreec/freec2circos/main.nf +++ b/tests/modules/nf-core/controlfreec/freec2circos/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../modules/nf-core/controlfreec/freec2circos/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../../modules/nf-core/controlfreec/freec2circos/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_freec2circos { diff --git a/tests/modules/nf-core/controlfreec/makegraph/main.nf b/tests/modules/nf-core/controlfreec/makegraph/main.nf index 2ff569578e0..a87285df741 100644 --- a/tests/modules/nf-core/controlfreec/makegraph/main.nf +++ b/tests/modules/nf-core/controlfreec/makegraph/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/nf-core/controlfreec/makegraph/main.nf' -include { CONTROLFREEC_FREEC } from '../../../../modules/nf-core/controlfreec/freec/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { CONTROLFREEC_MAKEGRAPH } from '../../../../../modules/nf-core/controlfreec/makegraph/main.nf' +include { CONTROLFREEC_FREEC } from '../../../../../modules/nf-core/controlfreec/freec/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' workflow test_controlfreec_makegraph { diff --git a/tests/modules/nf-core/cooler/cload/main.nf b/tests/modules/nf-core/cooler/cload/main.nf index a01e62e082c..baa0ea26272 100644 --- a/tests/modules/nf-core/cooler/cload/main.nf +++ b/tests/modules/nf-core/cooler/cload/main.nf @@ -2,12 +2,12 @@ nextflow.enable.dsl = 2 -include { COOLER_CLOAD } from '../../../../modules/nf-core/cooler/cload/main.nf' -include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/nf-core/cooler/cload/main.nf' -include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/nf-core/cooler/cload/main.nf' -include { COOLER_DUMP } from '../../../../modules/nf-core/cooler/dump/main.nf' -include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../modules/nf-core/cooler/dump/main.nf' -include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_CLOAD } from '../../../../../modules/nf-core/cooler/cload/main.nf' +include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../../modules/nf-core/cooler/cload/main.nf' +include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../../modules/nf-core/cooler/cload/main.nf' +include { COOLER_DUMP } from '../../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../../modules/nf-core/cooler/dump/main.nf' workflow test_cooler_cload_pairix { diff --git a/tests/modules/nf-core/cooler/digest/main.nf b/tests/modules/nf-core/cooler/digest/main.nf index e681d9d690b..bd2fd8a9ef7 100644 --- a/tests/modules/nf-core/cooler/digest/main.nf +++ b/tests/modules/nf-core/cooler/digest/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { COOLER_DIGEST } from '../../../../modules/nf-core/cooler/digest/main.nf' +include { COOLER_DIGEST } from '../../../../../modules/nf-core/cooler/digest/main.nf' workflow test_cooler_digest { diff --git a/tests/modules/nf-core/cooler/dump/main.nf b/tests/modules/nf-core/cooler/dump/main.nf index b93fe88b6fc..0b3c5e9fdb5 100644 --- a/tests/modules/nf-core/cooler/dump/main.nf +++ b/tests/modules/nf-core/cooler/dump/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { COOLER_DUMP } from '../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_DUMP } from '../../../../../modules/nf-core/cooler/dump/main.nf' workflow test_cooler_dump { diff --git a/tests/modules/nf-core/cooler/merge/main.nf b/tests/modules/nf-core/cooler/merge/main.nf index 294ef760db4..58ac789c264 100644 --- a/tests/modules/nf-core/cooler/merge/main.nf +++ b/tests/modules/nf-core/cooler/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { COOLER_MERGE } from '../../../../modules/nf-core/cooler/merge/main.nf' -include { COOLER_DUMP } from '../../../../modules/nf-core/cooler/dump/main.nf' +include { COOLER_MERGE } from '../../../../../modules/nf-core/cooler/merge/main.nf' +include { COOLER_DUMP } from '../../../../../modules/nf-core/cooler/dump/main.nf' workflow test_cooler_merge { diff --git a/tests/modules/nf-core/cooler/zoomify/main.nf b/tests/modules/nf-core/cooler/zoomify/main.nf index 1e21f18f994..5ec0a3296e2 100644 --- a/tests/modules/nf-core/cooler/zoomify/main.nf +++ b/tests/modules/nf-core/cooler/zoomify/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { COOLER_ZOOMIFY } from '../../../../modules/nf-core/cooler/zoomify/main.nf' +include { COOLER_ZOOMIFY } from '../../../../../modules/nf-core/cooler/zoomify/main.nf' workflow test_cooler_zoomify { diff --git a/tests/modules/nf-core/csvtk/concat/main.nf b/tests/modules/nf-core/csvtk/concat/main.nf index 606a5659e92..688e1258342 100644 --- a/tests/modules/nf-core/csvtk/concat/main.nf +++ b/tests/modules/nf-core/csvtk/concat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CSVTK_CONCAT } from '../../../../modules/nf-core/csvtk/concat/main.nf' +include { CSVTK_CONCAT } from '../../../../../modules/nf-core/csvtk/concat/main.nf' workflow test_csvtk_concat { diff --git a/tests/modules/nf-core/csvtk/split/main.nf b/tests/modules/nf-core/csvtk/split/main.nf index 14e78bb535e..3d373442ebb 100644 --- a/tests/modules/nf-core/csvtk/split/main.nf +++ b/tests/modules/nf-core/csvtk/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CSVTK_SPLIT } from '../../../../modules/nf-core/csvtk/split/main.nf' +include { CSVTK_SPLIT } from '../../../../../modules/nf-core/csvtk/split/main.nf' workflow test_csvtk_split_tsv { diff --git a/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf b/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf index 6b50b4fe636..33464d2ef51 100644 --- a/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/tests/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTQC } from '../../../../modules/nf-core/fastqc/main.nf' -include { MULTIQC } from '../../../../modules/nf-core/multiqc/main.nf' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/nf-core/custom/dumpsoftwareversions/main.nf' +include { FASTQC } from '../../../../../modules/nf-core/fastqc/main.nf' +include { MULTIQC } from '../../../../../modules/nf-core/multiqc/main.nf' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../../modules/nf-core/custom/dumpsoftwareversions/main.nf' workflow fastqc1 { take: diff --git a/tests/modules/nf-core/custom/getchromsizes/main.nf b/tests/modules/nf-core/custom/getchromsizes/main.nf index d0604def671..94413afcd5d 100644 --- a/tests/modules/nf-core/custom/getchromsizes/main.nf +++ b/tests/modules/nf-core/custom/getchromsizes/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CUSTOM_GETCHROMSIZES } from '../../../../modules/nf-core/custom/getchromsizes/main.nf' +include { CUSTOM_GETCHROMSIZES } from '../../../../../modules/nf-core/custom/getchromsizes/main.nf' workflow test_custom_getchromsizes { diff --git a/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf b/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf index 831a8f36a5e..399abb6eaec 100644 --- a/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf +++ b/tests/modules/nf-core/custom/sratoolsncbisettings/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/nf-core/custom/sratoolsncbisettings/main.nf' +include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../../modules/nf-core/custom/sratoolsncbisettings/main.nf' workflow test_sratoolsncbisettings_with_good_existing { diff --git a/tests/modules/nf-core/cutadapt/main.nf b/tests/modules/nf-core/cutadapt/main.nf index 2a986586441..edd1cde1a63 100644 --- a/tests/modules/nf-core/cutadapt/main.nf +++ b/tests/modules/nf-core/cutadapt/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { CUTADAPT } from '../../../modules/nf-core/cutadapt/main.nf' +include { CUTADAPT } from '../../../../modules/nf-core/cutadapt/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/damageprofiler/main.nf b/tests/modules/nf-core/damageprofiler/main.nf index f4be3ddad24..128bc52124f 100644 --- a/tests/modules/nf-core/damageprofiler/main.nf +++ b/tests/modules/nf-core/damageprofiler/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DAMAGEPROFILER } from '../../../modules/nf-core/damageprofiler/main.nf' +include { DAMAGEPROFILER } from '../../../../modules/nf-core/damageprofiler/main.nf' workflow test_damageprofiler { diff --git a/tests/modules/nf-core/dastool/dastool/main.nf b/tests/modules/nf-core/dastool/dastool/main.nf index 5327755a76d..efea6dc8436 100644 --- a/tests/modules/nf-core/dastool/dastool/main.nf +++ b/tests/modules/nf-core/dastool/dastool/main.nf @@ -1,10 +1,10 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf' -include { DASTOOL_DASTOOL } from '../../../../modules/nf-core/dastool/dastool/main.nf' +include { METABAT2_METABAT2 } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf' +include { DASTOOL_DASTOOL } from '../../../../../modules/nf-core/dastool/dastool/main.nf' workflow test_dastool_dastool { diff --git a/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf b/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf index ef27da91d93..70ea9bdafa8 100644 --- a/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf +++ b/tests/modules/nf-core/dastool/fastatocontig2bin/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' -include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf' +include { GUNZIP } from '../../../../../modules/nf-core/gunzip/main.nf' +include { METABAT2_METABAT2 } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../../modules/nf-core/dastool/fastatocontig2bin/main.nf' workflow test_dastool_fastatocontig2bin { diff --git a/tests/modules/nf-core/dastool/scaffolds2bin/main.nf b/tests/modules/nf-core/dastool/scaffolds2bin/main.nf index 7fc81d90ccd..272b7abf685 100644 --- a/tests/modules/nf-core/dastool/scaffolds2bin/main.nf +++ b/tests/modules/nf-core/dastool/scaffolds2bin/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' -include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/nf-core/dastool/scaffolds2bin/main.nf' +include { GUNZIP } from '../../../../../modules/nf-core/gunzip/main.nf' +include { METABAT2_METABAT2 } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_SCAFFOLDS2BIN } from '../../../../../modules/nf-core/dastool/scaffolds2bin/main.nf' workflow test_dastool_scaffolds2bin { diff --git a/tests/modules/nf-core/dedup/main.nf b/tests/modules/nf-core/dedup/main.nf index 5e2eb5a63f8..0d8b89b9626 100644 --- a/tests/modules/nf-core/dedup/main.nf +++ b/tests/modules/nf-core/dedup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEDUP } from '../../../modules/nf-core/dedup/main.nf' +include { DEDUP } from '../../../../modules/nf-core/dedup/main.nf' workflow test_dedup { diff --git a/tests/modules/nf-core/deeparg/downloaddata/main.nf b/tests/modules/nf-core/deeparg/downloaddata/main.nf index 523a81ffcdd..eecbdabc8da 100644 --- a/tests/modules/nf-core/deeparg/downloaddata/main.nf +++ b/tests/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPARG_DOWNLOADDATA } from '../../../../modules/nf-core/deeparg/downloaddata/main.nf' +include { DEEPARG_DOWNLOADDATA } from '../../../../../modules/nf-core/deeparg/downloaddata/main.nf' workflow test_deeparg_downloaddata { DEEPARG_DOWNLOADDATA ( ) diff --git a/tests/modules/nf-core/deeparg/predict/main.nf b/tests/modules/nf-core/deeparg/predict/main.nf index 40247a35bb8..5037e398d1e 100644 --- a/tests/modules/nf-core/deeparg/predict/main.nf +++ b/tests/modules/nf-core/deeparg/predict/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DEEPARG_DOWNLOADDATA } from '../../../../modules/nf-core/deeparg/downloaddata/main.nf' -include { DEEPARG_PREDICT } from '../../../../modules/nf-core/deeparg/predict/main.nf' +include { DEEPARG_DOWNLOADDATA } from '../../../../../modules/nf-core/deeparg/downloaddata/main.nf' +include { DEEPARG_PREDICT } from '../../../../../modules/nf-core/deeparg/predict/main.nf' workflow test_deeparg_predict { diff --git a/tests/modules/nf-core/deepbgc/download/main.nf b/tests/modules/nf-core/deepbgc/download/main.nf index 30094cccf14..cfa71428370 100644 --- a/tests/modules/nf-core/deepbgc/download/main.nf +++ b/tests/modules/nf-core/deepbgc/download/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPBGC_DOWNLOAD } from '../../../../modules/nf-core/deepbgc/download/main.nf' +include { DEEPBGC_DOWNLOAD } from '../../../../../modules/nf-core/deepbgc/download/main.nf' workflow test_deepbgc_download { diff --git a/tests/modules/nf-core/deepbgc/pipeline/main.nf b/tests/modules/nf-core/deepbgc/pipeline/main.nf index a68cc33d62b..41b103d9e2a 100644 --- a/tests/modules/nf-core/deepbgc/pipeline/main.nf +++ b/tests/modules/nf-core/deepbgc/pipeline/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' -include { PRODIGAL } from '../../../modules/nf-core/prodigal/main.nf' -include { DEEPBGC_DOWNLOAD } from '../../../../modules/nf-core/deepbgc/download/main.nf' -include { DEEPBGC_PIPELINE } from '../../../../modules/nf-core/deepbgc/pipeline/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { PRODIGAL } from '../../../../modules/nf-core/prodigal/main.nf' +include { DEEPBGC_DOWNLOAD } from '../../../../../modules/nf-core/deepbgc/download/main.nf' +include { DEEPBGC_PIPELINE } from '../../../../../modules/nf-core/deepbgc/pipeline/main.nf' workflow test_deepbgc_pipeline_gbk { diff --git a/tests/modules/nf-core/deeptools/bamcoverage/main.nf b/tests/modules/nf-core/deeptools/bamcoverage/main.nf index 202edce08db..170476944e8 100644 --- a/tests/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/tests/modules/nf-core/deeptools/bamcoverage/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/nf-core/deeptools/bamcoverage/main.nf' +include { DEEPTOOLS_BAMCOVERAGE } from '../../../../../modules/nf-core/deeptools/bamcoverage/main.nf' workflow test_deeptools_bamcoverage_bam { diff --git a/tests/modules/nf-core/deeptools/computematrix/main.nf b/tests/modules/nf-core/deeptools/computematrix/main.nf index 1f9d9232a90..57a2baf20cf 100644 --- a/tests/modules/nf-core/deeptools/computematrix/main.nf +++ b/tests/modules/nf-core/deeptools/computematrix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../modules/nf-core/deeptools/computematrix/main.nf' +include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../../modules/nf-core/deeptools/computematrix/main.nf' workflow test_deeptools_computematrix { diff --git a/tests/modules/nf-core/deeptools/plotfingerprint/main.nf b/tests/modules/nf-core/deeptools/plotfingerprint/main.nf index 1fe414e6e9b..6b77c173b3d 100644 --- a/tests/modules/nf-core/deeptools/plotfingerprint/main.nf +++ b/tests/modules/nf-core/deeptools/plotfingerprint/main.nf @@ -4,7 +4,7 @@ nextflow.enable.dsl = 2 params.fragment_size = 1000 -include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../modules/nf-core/deeptools/plotfingerprint/main.nf' +include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../../modules/nf-core/deeptools/plotfingerprint/main.nf' workflow test_deeptools_plotfingerprint { diff --git a/tests/modules/nf-core/deeptools/plotheatmap/main.nf b/tests/modules/nf-core/deeptools/plotheatmap/main.nf index b553cbd74fb..7c178278cbe 100644 --- a/tests/modules/nf-core/deeptools/plotheatmap/main.nf +++ b/tests/modules/nf-core/deeptools/plotheatmap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_PLOTHEATMAP } from '../../../../modules/nf-core/deeptools/plotheatmap/main.nf' +include { DEEPTOOLS_PLOTHEATMAP } from '../../../../../modules/nf-core/deeptools/plotheatmap/main.nf' workflow test_deeptools_plotheatmap { diff --git a/tests/modules/nf-core/deeptools/plotprofile/main.nf b/tests/modules/nf-core/deeptools/plotprofile/main.nf index 573310a4c14..d1bff6276a8 100644 --- a/tests/modules/nf-core/deeptools/plotprofile/main.nf +++ b/tests/modules/nf-core/deeptools/plotprofile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DEEPTOOLS_PLOTPROFILE } from '../../../../modules/nf-core/deeptools/plotprofile/main.nf' +include { DEEPTOOLS_PLOTPROFILE } from '../../../../../modules/nf-core/deeptools/plotprofile/main.nf' workflow test_deeptools_plotprofile { diff --git a/tests/modules/nf-core/deepvariant/main.nf b/tests/modules/nf-core/deepvariant/main.nf index b430ea07831..f6fb857c848 100644 --- a/tests/modules/nf-core/deepvariant/main.nf +++ b/tests/modules/nf-core/deepvariant/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant/main.nf' -include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/nf-core/deepvariant/main.nf' +include { DEEPVARIANT } from '../../../../modules/nf-core/deepvariant/main.nf' +include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../../modules/nf-core/deepvariant/main.nf' workflow test_deepvariant { diff --git a/tests/modules/nf-core/delly/call/main.nf b/tests/modules/nf-core/delly/call/main.nf index 71298935676..8be4b492c1f 100644 --- a/tests/modules/nf-core/delly/call/main.nf +++ b/tests/modules/nf-core/delly/call/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DELLY_CALL } from '../../../../modules/nf-core/delly/call/main.nf' +include { DELLY_CALL } from '../../../../../modules/nf-core/delly/call/main.nf' workflow test_delly_call_bam { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/diamond/blastp/main.nf b/tests/modules/nf-core/diamond/blastp/main.nf index c9d676e1631..0e890f5a5a0 100644 --- a/tests/modules/nf-core/diamond/blastp/main.nf +++ b/tests/modules/nf-core/diamond/blastp/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' -include { DIAMOND_BLASTP } from '../../../../modules/nf-core/diamond/blastp/main.nf' +include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_BLASTP } from '../../../../../modules/nf-core/diamond/blastp/main.nf' workflow test_diamond_blastp { diff --git a/tests/modules/nf-core/diamond/blastx/main.nf b/tests/modules/nf-core/diamond/blastx/main.nf index 86d23a83597..5fdc8e63c7e 100644 --- a/tests/modules/nf-core/diamond/blastx/main.nf +++ b/tests/modules/nf-core/diamond/blastx/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' -include { DIAMOND_BLASTX } from '../../../../modules/nf-core/diamond/blastx/main.nf' +include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_BLASTX } from '../../../../../modules/nf-core/diamond/blastx/main.nf' workflow test_diamond_blastx { diff --git a/tests/modules/nf-core/diamond/makedb/main.nf b/tests/modules/nf-core/diamond/makedb/main.nf index 30fcab92f97..6276ba4733c 100644 --- a/tests/modules/nf-core/diamond/makedb/main.nf +++ b/tests/modules/nf-core/diamond/makedb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf' workflow test_diamond_makedb { diff --git a/tests/modules/nf-core/dragmap/align/main.nf b/tests/modules/nf-core/dragmap/align/main.nf index bb4e78de7a9..55d47fa5c4e 100644 --- a/tests/modules/nf-core/dragmap/align/main.nf +++ b/tests/modules/nf-core/dragmap/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DRAGMAP_HASHTABLE } from '../../../../modules/nf-core/dragmap/hashtable/main.nf' -include { DRAGMAP_ALIGN } from '../../../../modules/nf-core/dragmap/align/main.nf' +include { DRAGMAP_HASHTABLE } from '../../../../../modules/nf-core/dragmap/hashtable/main.nf' +include { DRAGMAP_ALIGN } from '../../../../../modules/nf-core/dragmap/align/main.nf' workflow test_dragmap_align_single_end { input = [ diff --git a/tests/modules/nf-core/dragmap/hashtable/main.nf b/tests/modules/nf-core/dragmap/hashtable/main.nf index e26d1474769..7e72f66f828 100644 --- a/tests/modules/nf-core/dragmap/hashtable/main.nf +++ b/tests/modules/nf-core/dragmap/hashtable/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DRAGMAP_HASHTABLE } from '../../../../modules/nf-core/dragmap/hashtable/main.nf' +include { DRAGMAP_HASHTABLE } from '../../../../../modules/nf-core/dragmap/hashtable/main.nf' workflow test_dragmap_hashtable { diff --git a/tests/modules/nf-core/dragonflye/main.nf b/tests/modules/nf-core/dragonflye/main.nf index 2073a41fec7..a52287c1c25 100644 --- a/tests/modules/nf-core/dragonflye/main.nf +++ b/tests/modules/nf-core/dragonflye/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { DRAGONFLYE } from '../../../modules/nf-core/dragonflye/main.nf' -include { DRAGONFLYE as DRAGONFLYE_RAVEN } from '../../../modules/nf-core/dragonflye/main.nf' +include { DRAGONFLYE } from '../../../../modules/nf-core/dragonflye/main.nf' +include { DRAGONFLYE as DRAGONFLYE_RAVEN } from '../../../../modules/nf-core/dragonflye/main.nf' workflow test_dragonflye { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/dshbio/exportsegments/main.nf b/tests/modules/nf-core/dshbio/exportsegments/main.nf index c4447dc1ae3..2d1a3d98d4c 100644 --- a/tests/modules/nf-core/dshbio/exportsegments/main.nf +++ b/tests/modules/nf-core/dshbio/exportsegments/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_EXPORTSEGMENTS } from '../../../../modules/nf-core/dshbio/exportsegments/main.nf' +include { DSHBIO_EXPORTSEGMENTS } from '../../../../../modules/nf-core/dshbio/exportsegments/main.nf' workflow test_dshbio_exportsegments { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/filterbed/main.nf b/tests/modules/nf-core/dshbio/filterbed/main.nf index e4efaaa7057..9b0313fe42c 100644 --- a/tests/modules/nf-core/dshbio/filterbed/main.nf +++ b/tests/modules/nf-core/dshbio/filterbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_FILTERBED } from '../../../../modules/nf-core/dshbio/filterbed/main.nf' +include { DSHBIO_FILTERBED } from '../../../../../modules/nf-core/dshbio/filterbed/main.nf' workflow test_dshbio_filterbed { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/filtergff3/main.nf b/tests/modules/nf-core/dshbio/filtergff3/main.nf index 1337c030f3c..5d679b77a6d 100644 --- a/tests/modules/nf-core/dshbio/filtergff3/main.nf +++ b/tests/modules/nf-core/dshbio/filtergff3/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_FILTERGFF3 } from '../../../../modules/nf-core/dshbio/filtergff3/main.nf' +include { DSHBIO_FILTERGFF3 } from '../../../../../modules/nf-core/dshbio/filtergff3/main.nf' workflow test_dshbio_filtergff3 { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/splitbed/main.nf b/tests/modules/nf-core/dshbio/splitbed/main.nf index e70c5235534..bc9bd7acbeb 100644 --- a/tests/modules/nf-core/dshbio/splitbed/main.nf +++ b/tests/modules/nf-core/dshbio/splitbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_SPLITBED } from '../../../../modules/nf-core/dshbio/splitbed/main.nf' +include { DSHBIO_SPLITBED } from '../../../../../modules/nf-core/dshbio/splitbed/main.nf' workflow test_dshbio_splitbed { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/dshbio/splitgff3/main.nf b/tests/modules/nf-core/dshbio/splitgff3/main.nf index e9f9f302585..4cdc70f6701 100644 --- a/tests/modules/nf-core/dshbio/splitgff3/main.nf +++ b/tests/modules/nf-core/dshbio/splitgff3/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { DSHBIO_SPLITGFF3 } from '../../../../modules/nf-core/dshbio/splitgff3/main.nf' +include { DSHBIO_SPLITGFF3 } from '../../../../../modules/nf-core/dshbio/splitgff3/main.nf' workflow test_dshbio_splitgff3 { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/ectyper/main.nf b/tests/modules/nf-core/ectyper/main.nf index 3279d8358d7..4f23616e918 100644 --- a/tests/modules/nf-core/ectyper/main.nf +++ b/tests/modules/nf-core/ectyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ECTYPER } from '../../../modules/nf-core/ectyper/main.nf' +include { ECTYPER } from '../../../../modules/nf-core/ectyper/main.nf' workflow test_ectyper { diff --git a/tests/modules/nf-core/eido/convert/main.nf b/tests/modules/nf-core/eido/convert/main.nf index 2eb26b4c4c1..6af8cff274b 100644 --- a/tests/modules/nf-core/eido/convert/main.nf +++ b/tests/modules/nf-core/eido/convert/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EIDO_CONVERT } from '../../../../modules/nf-core/eido/convert/main.nf' +include { EIDO_CONVERT } from '../../../../../modules/nf-core/eido/convert/main.nf' workflow test_eido_convert_nextflow_samplesheet { diff --git a/tests/modules/nf-core/eido/validate/main.nf b/tests/modules/nf-core/eido/validate/main.nf index 24400e9304d..3867adc123b 100644 --- a/tests/modules/nf-core/eido/validate/main.nf +++ b/tests/modules/nf-core/eido/validate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EIDO_VALIDATE } from '../../../../modules/nf-core/eido/validate/main.nf' +include { EIDO_VALIDATE } from '../../../../../modules/nf-core/eido/validate/main.nf' workflow test_eido_validate_on_nextflow_samplesheet { diff --git a/tests/modules/nf-core/elprep/filter/main.nf b/tests/modules/nf-core/elprep/filter/main.nf index 72bc27fe45a..834198a46fa 100644 --- a/tests/modules/nf-core/elprep/filter/main.nf +++ b/tests/modules/nf-core/elprep/filter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ELPREP_FILTER } from '../../../../modules/nf-core/elprep/filter/main.nf' +include { ELPREP_FILTER } from '../../../../../modules/nf-core/elprep/filter/main.nf' workflow test_elprep_filter { diff --git a/tests/modules/nf-core/elprep/merge/main.nf b/tests/modules/nf-core/elprep/merge/main.nf index 7f74d38f723..71dfb0708d1 100644 --- a/tests/modules/nf-core/elprep/merge/main.nf +++ b/tests/modules/nf-core/elprep/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ELPREP_SPLIT } from '../../../../modules/nf-core/elprep/split/main.nf' -include { ELPREP_MERGE } from '../../../../modules/nf-core/elprep/merge/main.nf' +include { ELPREP_SPLIT } from '../../../../../modules/nf-core/elprep/split/main.nf' +include { ELPREP_MERGE } from '../../../../../modules/nf-core/elprep/merge/main.nf' workflow test_elprep_merge { diff --git a/tests/modules/nf-core/elprep/split/main.nf b/tests/modules/nf-core/elprep/split/main.nf index de98c390f3c..3fc26986417 100644 --- a/tests/modules/nf-core/elprep/split/main.nf +++ b/tests/modules/nf-core/elprep/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ELPREP_SPLIT } from '../../../../modules/nf-core/elprep/split/main.nf' +include { ELPREP_SPLIT } from '../../../../../modules/nf-core/elprep/split/main.nf' workflow test_elprep_split { diff --git a/tests/modules/nf-core/emboss/seqret/main.nf b/tests/modules/nf-core/emboss/seqret/main.nf index bc9193f76f8..1648c0d1677 100644 --- a/tests/modules/nf-core/emboss/seqret/main.nf +++ b/tests/modules/nf-core/emboss/seqret/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { EMBOSS_SEQRET } from '../../../../modules/nf-core/emboss/seqret/main.nf' -include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' +include { EMBOSS_SEQRET } from '../../../../../modules/nf-core/emboss/seqret/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' workflow test_emboss_seqret_gb2embl { diff --git a/tests/modules/nf-core/emmtyper/main.nf b/tests/modules/nf-core/emmtyper/main.nf index 68bd23dda35..b2cd94d552b 100644 --- a/tests/modules/nf-core/emmtyper/main.nf +++ b/tests/modules/nf-core/emmtyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EMMTYPER } from '../../../modules/nf-core/emmtyper/main.nf' +include { EMMTYPER } from '../../../../modules/nf-core/emmtyper/main.nf' workflow test_emmtyper { diff --git a/tests/modules/nf-core/endorspy/main.nf b/tests/modules/nf-core/endorspy/main.nf index 63cedef11bd..0b9da1335ab 100644 --- a/tests/modules/nf-core/endorspy/main.nf +++ b/tests/modules/nf-core/endorspy/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { ENDORSPY } from '../../../modules/nf-core/endorspy/main.nf' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main.nf' -include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../modules/nf-core/samtools/flagstat/main.nf' -include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main.nf' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main.nf' +include { ENDORSPY } from '../../../../modules/nf-core/endorspy/main.nf' +include { SAMTOOLS_FLAGSTAT } from '../../../../modules/nf-core/samtools/flagstat/main.nf' +include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../../modules/nf-core/samtools/flagstat/main.nf' +include { SAMTOOLS_VIEW } from '../../../../modules/nf-core/samtools/view/main.nf' +include { SAMTOOLS_INDEX } from '../../../../modules/nf-core/samtools/index/main.nf' workflow test_endorspy { diff --git a/tests/modules/nf-core/ensemblvep/main.nf b/tests/modules/nf-core/ensemblvep/main.nf index 88d63232bfa..c1f89406a5f 100644 --- a/tests/modules/nf-core/ensemblvep/main.nf +++ b/tests/modules/nf-core/ensemblvep/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { ENSEMBLVEP } from '../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP } from '../../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } from '../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../../modules/nf-core/ensemblvep/main.nf' +include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } from '../../../../modules/nf-core/ensemblvep/main.nf' workflow test_ensemblvep_fasta_json { input = [ diff --git a/tests/modules/nf-core/entrezdirect/esummary/main.nf b/tests/modules/nf-core/entrezdirect/esummary/main.nf index f86f7c77544..a951496f42a 100644 --- a/tests/modules/nf-core/entrezdirect/esummary/main.nf +++ b/tests/modules/nf-core/entrezdirect/esummary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/nf-core/entrezdirect/esummary/main.nf' +include { ENTREZDIRECT_ESUMMARY } from '../../../../../modules/nf-core/entrezdirect/esummary/main.nf' // // Test with SRA database diff --git a/tests/modules/nf-core/entrezdirect/xtract/main.nf b/tests/modules/nf-core/entrezdirect/xtract/main.nf index 934fc2e6e62..f56ef23f50c 100644 --- a/tests/modules/nf-core/entrezdirect/xtract/main.nf +++ b/tests/modules/nf-core/entrezdirect/xtract/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ENTREZDIRECT_ESUMMARY } from '../../../../modules/nf-core/entrezdirect/esummary/main.nf' -include { ENTREZDIRECT_XTRACT } from '../../../../modules/nf-core/entrezdirect/xtract/main.nf' +include { ENTREZDIRECT_ESUMMARY } from '../../../../../modules/nf-core/entrezdirect/esummary/main.nf' +include { ENTREZDIRECT_XTRACT } from '../../../../../modules/nf-core/entrezdirect/xtract/main.nf' // // Test with Assembly database diff --git a/tests/modules/nf-core/epang/main.nf b/tests/modules/nf-core/epang/main.nf index 5496ffe4047..9cb84cdcc89 100644 --- a/tests/modules/nf-core/epang/main.nf +++ b/tests/modules/nf-core/epang/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EPANG } from '../../../modules/nf-core/epang/main.nf' +include { EPANG } from '../../../../modules/nf-core/epang/main.nf' workflow test_epang { diff --git a/tests/modules/nf-core/expansionhunter/main.nf b/tests/modules/nf-core/expansionhunter/main.nf index 1f5a41edeab..2674e54b163 100644 --- a/tests/modules/nf-core/expansionhunter/main.nf +++ b/tests/modules/nf-core/expansionhunter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { EXPANSIONHUNTER } from '../../../modules/nf-core/expansionhunter/main.nf' +include { EXPANSIONHUNTER } from '../../../../modules/nf-core/expansionhunter/main.nf' workflow test_expansionhunter { diff --git a/tests/modules/nf-core/faqcs/main.nf b/tests/modules/nf-core/faqcs/main.nf index 06e12c5de45..1f374c1c343 100644 --- a/tests/modules/nf-core/faqcs/main.nf +++ b/tests/modules/nf-core/faqcs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FAQCS } from '../../../modules/nf-core/faqcs/main.nf' +include { FAQCS } from '../../../../modules/nf-core/faqcs/main.nf' // diff --git a/tests/modules/nf-core/fargene/main.nf b/tests/modules/nf-core/fargene/main.nf index aecdbf67254..daebcb3aa37 100644 --- a/tests/modules/nf-core/fargene/main.nf +++ b/tests/modules/nf-core/fargene/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' -include { FARGENE } from '../../../modules/nf-core/fargene/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { FARGENE } from '../../../../modules/nf-core/fargene/main.nf' workflow test_fargene { diff --git a/tests/modules/nf-core/fastani/main.nf b/tests/modules/nf-core/fastani/main.nf index bb20fa296d4..8538ebc369e 100644 --- a/tests/modules/nf-core/fastani/main.nf +++ b/tests/modules/nf-core/fastani/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTANI } from '../../../modules/nf-core/fastani/main.nf' +include { FASTANI } from '../../../../modules/nf-core/fastani/main.nf' workflow test_fastani { diff --git a/tests/modules/nf-core/fastawindows/main.nf b/tests/modules/nf-core/fastawindows/main.nf index 8abccb01b65..b3448fc3855 100644 --- a/tests/modules/nf-core/fastawindows/main.nf +++ b/tests/modules/nf-core/fastawindows/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTAWINDOWS } from '../../../modules/nf-core/fastawindows/main.nf' +include { FASTAWINDOWS } from '../../../../modules/nf-core/fastawindows/main.nf' workflow test_fastawindows { diff --git a/tests/modules/nf-core/fastk/fastk/main.nf b/tests/modules/nf-core/fastk/fastk/main.nf index e00102f92cd..aa30d58890a 100644 --- a/tests/modules/nf-core/fastk/fastk/main.nf +++ b/tests/modules/nf-core/fastk/fastk/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf' workflow test_fastk_fastk_single_end { diff --git a/tests/modules/nf-core/fastk/histex/main.nf b/tests/modules/nf-core/fastk/histex/main.nf index c4656df5879..cc0f3f8ae79 100644 --- a/tests/modules/nf-core/fastk/histex/main.nf +++ b/tests/modules/nf-core/fastk/histex/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { FASTK_HISTEX } from '../../../../modules/nf-core/fastk/histex/main.nf' +include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_HISTEX } from '../../../../../modules/nf-core/fastk/histex/main.nf' workflow test_fastk_histex { diff --git a/tests/modules/nf-core/fastk/merge/main.nf b/tests/modules/nf-core/fastk/merge/main.nf index abccfc74507..9ff9b338bae 100644 --- a/tests/modules/nf-core/fastk/merge/main.nf +++ b/tests/modules/nf-core/fastk/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { FASTK_MERGE } from '../../../../modules/nf-core/fastk/merge/main.nf' +include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_MERGE } from '../../../../../modules/nf-core/fastk/merge/main.nf' workflow test_fastk_merge_hist_only { diff --git a/tests/modules/nf-core/fastp/main.nf b/tests/modules/nf-core/fastp/main.nf index e5fa3badf45..6d433e25825 100644 --- a/tests/modules/nf-core/fastp/main.nf +++ b/tests/modules/nf-core/fastp/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTP } from '../../../modules/nf-core/fastp/main.nf' +include { FASTP } from '../../../../modules/nf-core/fastp/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/fastqc/main.nf b/tests/modules/nf-core/fastqc/main.nf index fc13cb97a1f..ebb3660f761 100644 --- a/tests/modules/nf-core/fastqc/main.nf +++ b/tests/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTQC } from '../../../modules/nf-core/fastqc/main.nf' +include { FASTQC } from '../../../../modules/nf-core/fastqc/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/fastqscan/main.nf b/tests/modules/nf-core/fastqscan/main.nf index d5b517a6bdc..a51053efab6 100644 --- a/tests/modules/nf-core/fastqscan/main.nf +++ b/tests/modules/nf-core/fastqscan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTQSCAN } from '../../../modules/nf-core/fastqscan/main.nf' +include { FASTQSCAN } from '../../../../modules/nf-core/fastqscan/main.nf' workflow test_fastqscan { diff --git a/tests/modules/nf-core/fasttree/main.nf b/tests/modules/nf-core/fasttree/main.nf index c61a56df07d..a7ce7f0d214 100644 --- a/tests/modules/nf-core/fasttree/main.nf +++ b/tests/modules/nf-core/fasttree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FASTTREE } from '../../../modules/nf-core/fasttree/main.nf' +include { FASTTREE } from '../../../../modules/nf-core/fasttree/main.nf' workflow test_fasttree { diff --git a/tests/modules/nf-core/fcs/fcsadaptor/main.nf b/tests/modules/nf-core/fcs/fcsadaptor/main.nf index 1101e5c8731..b6f38e0d8d6 100644 --- a/tests/modules/nf-core/fcs/fcsadaptor/main.nf +++ b/tests/modules/nf-core/fcs/fcsadaptor/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FCS_FCSADAPTOR } from '../../../../modules/nf-core/fcs/fcsadaptor/main.nf' +include { FCS_FCSADAPTOR } from '../../../../../modules/nf-core/fcs/fcsadaptor/main.nf' workflow test_fcs_fcsadaptor { diff --git a/tests/modules/nf-core/ffq/main.nf b/tests/modules/nf-core/ffq/main.nf index 92725f7a5fd..1546fc97599 100644 --- a/tests/modules/nf-core/ffq/main.nf +++ b/tests/modules/nf-core/ffq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FFQ } from '../../../modules/nf-core/ffq/main.nf' +include { FFQ } from '../../../../modules/nf-core/ffq/main.nf' workflow test_ffq_single_id { diff --git a/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index af06b72091d..33364cc85e7 100644 --- a/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/tests/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FGBIO_SORTBAM } from '../../../../modules/nf-core/fgbio/sortbam/main.nf' -include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf' +include { FGBIO_SORTBAM } from '../../../../../modules/nf-core/fgbio/sortbam/main.nf' +include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf' workflow test_fgbio_callmolecularconsensusreads { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/fgbio/fastqtobam/main.nf b/tests/modules/nf-core/fgbio/fastqtobam/main.nf index b50eb2d91b6..79d58ebad46 100644 --- a/tests/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/tests/modules/nf-core/fgbio/fastqtobam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FGBIO_FASTQTOBAM } from '../../../../modules/nf-core/fgbio/fastqtobam/main.nf' +include { FGBIO_FASTQTOBAM } from '../../../../../modules/nf-core/fgbio/fastqtobam/main.nf' workflow test_fgbio_fastqtobam_paired_default { diff --git a/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf index d992a1a0347..8082f60168d 100644 --- a/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/tests/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/nf-core/fgbio/groupreadsbyumi/main.nf' +include { FGBIO_GROUPREADSBYUMI } from '../../../../../modules/nf-core/fgbio/groupreadsbyumi/main.nf' workflow test_fgbio_groupreadsbyumi { diff --git a/tests/modules/nf-core/fgbio/sortbam/main.nf b/tests/modules/nf-core/fgbio/sortbam/main.nf index d153d819961..99d78230d7f 100644 --- a/tests/modules/nf-core/fgbio/sortbam/main.nf +++ b/tests/modules/nf-core/fgbio/sortbam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FGBIO_SORTBAM } from '../../../../modules/nf-core/fgbio/sortbam/main.nf' +include { FGBIO_SORTBAM } from '../../../../../modules/nf-core/fgbio/sortbam/main.nf' workflow test_fgbio_sortbam { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/filtlong/main.nf b/tests/modules/nf-core/filtlong/main.nf index 0499278a487..cf45097145b 100644 --- a/tests/modules/nf-core/filtlong/main.nf +++ b/tests/modules/nf-core/filtlong/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FILTLONG } from '../../../modules/nf-core/filtlong/main.nf' +include { FILTLONG } from '../../../../modules/nf-core/filtlong/main.nf' workflow test_filtlong { diff --git a/tests/modules/nf-core/flash/main.nf b/tests/modules/nf-core/flash/main.nf index 5d183e9d0bc..2e3bd94c858 100644 --- a/tests/modules/nf-core/flash/main.nf +++ b/tests/modules/nf-core/flash/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FLASH } from '../../../modules/nf-core/flash/main.nf' +include { FLASH } from '../../../../modules/nf-core/flash/main.nf' workflow test_flash { input = [ diff --git a/tests/modules/nf-core/flye/main.nf b/tests/modules/nf-core/flye/main.nf index 6fef10bec2a..aef37343ecf 100644 --- a/tests/modules/nf-core/flye/main.nf +++ b/tests/modules/nf-core/flye/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FLYE } from '../../../modules/nf-core/flye/main.nf' +include { FLYE } from '../../../../modules/nf-core/flye/main.nf' workflow test_flye_pacbio_raw { diff --git a/tests/modules/nf-core/fq/lint/main.nf b/tests/modules/nf-core/fq/lint/main.nf index 91c6350b151..97a18da7910 100644 --- a/tests/modules/nf-core/fq/lint/main.nf +++ b/tests/modules/nf-core/fq/lint/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FQ_LINT } from '../../../../modules/nf-core/fq/lint/main.nf' +include { FQ_LINT } from '../../../../../modules/nf-core/fq/lint/main.nf' workflow test_fq_lint_success { diff --git a/tests/modules/nf-core/freebayes/main.nf b/tests/modules/nf-core/freebayes/main.nf index 472b00d2d91..4c4a1031f34 100644 --- a/tests/modules/nf-core/freebayes/main.nf +++ b/tests/modules/nf-core/freebayes/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { FREEBAYES } from '../../../modules/nf-core/freebayes/main.nf' +include { FREEBAYES } from '../../../../modules/nf-core/freebayes/main.nf' workflow test_freebayes { targets = [] diff --git a/tests/modules/nf-core/gamma/gamma/main.nf b/tests/modules/nf-core/gamma/gamma/main.nf index 2e90bb437c0..f8158a5e81c 100644 --- a/tests/modules/nf-core/gamma/gamma/main.nf +++ b/tests/modules/nf-core/gamma/gamma/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAMMA_GAMMA } from '../../../../modules/nf-core/gamma/gamma/main.nf' +include { GAMMA_GAMMA } from '../../../../../modules/nf-core/gamma/gamma/main.nf' workflow test_unzip { diff --git a/tests/modules/nf-core/gappa/examineassign/main.nf b/tests/modules/nf-core/gappa/examineassign/main.nf index e93135274e1..845393b5e49 100644 --- a/tests/modules/nf-core/gappa/examineassign/main.nf +++ b/tests/modules/nf-core/gappa/examineassign/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAPPA_EXAMINEASSIGN } from '../../../../modules/nf-core/gappa/examineassign/main.nf' +include { GAPPA_EXAMINEASSIGN } from '../../../../../modules/nf-core/gappa/examineassign/main.nf' workflow test_gappa_examineassign { diff --git a/tests/modules/nf-core/gappa/examinegraft/main.nf b/tests/modules/nf-core/gappa/examinegraft/main.nf index ea86db6d905..af3f74f4541 100644 --- a/tests/modules/nf-core/gappa/examinegraft/main.nf +++ b/tests/modules/nf-core/gappa/examinegraft/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAPPA_EXAMINEGRAFT } from '../../../../modules/nf-core/gappa/examinegraft/main.nf' +include { GAPPA_EXAMINEGRAFT } from '../../../../../modules/nf-core/gappa/examinegraft/main.nf' workflow test_gappa_examinegraft { diff --git a/tests/modules/nf-core/gappa/examineheattree/main.nf b/tests/modules/nf-core/gappa/examineheattree/main.nf index bc5a3d6a3e0..ce167497081 100644 --- a/tests/modules/nf-core/gappa/examineheattree/main.nf +++ b/tests/modules/nf-core/gappa/examineheattree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GAPPA_EXAMINEHEATTREE } from '../../../../modules/nf-core/gappa/examineheattree/main.nf' +include { GAPPA_EXAMINEHEATTREE } from '../../../../../modules/nf-core/gappa/examineheattree/main.nf' workflow test_gappa_examineheattree { diff --git a/tests/modules/nf-core/gatk/indelrealigner/main.nf b/tests/modules/nf-core/gatk/indelrealigner/main.nf index 9190d0f2a7b..ece32ead2e7 100644 --- a/tests/modules/nf-core/gatk/indelrealigner/main.nf +++ b/tests/modules/nf-core/gatk/indelrealigner/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/nf-core/gatk/realignertargetcreator/main.nf' -include { GATK_INDELREALIGNER } from '../../../../modules/nf-core/gatk/indelrealigner/main.nf' +include { GATK_REALIGNERTARGETCREATOR } from '../../../../../modules/nf-core/gatk/realignertargetcreator/main.nf' +include { GATK_INDELREALIGNER } from '../../../../../modules/nf-core/gatk/indelrealigner/main.nf' workflow test_gatk_indelrealigner { diff --git a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf index 1193f297707..9effbc9f80d 100644 --- a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/nf-core/gatk/realignertargetcreator/main.nf' +include { GATK_REALIGNERTARGETCREATOR } from '../../../../../modules/nf-core/gatk/realignertargetcreator/main.nf' workflow test_gatk_realignertargetcreator { diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf index f349ae67d8b..9d7fc80904f 100644 --- a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' +include { GATK_UNIFIEDGENOTYPER } from '../../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' workflow test_gatk_unifiedgenotyper { diff --git a/tests/modules/nf-core/gatk4/applybqsr/main.nf b/tests/modules/nf-core/gatk4/applybqsr/main.nf index dc7284776aa..78ca943e91d 100644 --- a/tests/modules/nf-core/gatk4/applybqsr/main.nf +++ b/tests/modules/nf-core/gatk4/applybqsr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYBQSR } from '../../../../modules/nf-core/gatk4/applybqsr/main.nf' +include { GATK4_APPLYBQSR } from '../../../../../modules/nf-core/gatk4/applybqsr/main.nf' workflow test_gatk4_applybqsr { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/main.nf b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf index 32f0b72dacf..32660254840 100644 --- a/tests/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYBQSR_SPARK } from '../../../../modules/nf-core/gatk4/applybqsrspark/main.nf' +include { GATK4_APPLYBQSR_SPARK } from '../../../../../modules/nf-core/gatk4/applybqsrspark/main.nf' workflow test_gatk4_applybqsr_spark { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/applyvqsr/main.nf b/tests/modules/nf-core/gatk4/applyvqsr/main.nf index 355b86e2871..ea209478555 100644 --- a/tests/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/tests/modules/nf-core/gatk4/applyvqsr/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/nf-core/gatk4/applyvqsr/main.nf' -include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/nf-core/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../../modules/nf-core/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../../modules/nf-core/gatk4/applyvqsr/main.nf' workflow test_gatk4_applyvqsr { input = [ [ id:'test'], // meta map diff --git a/tests/modules/nf-core/gatk4/baserecalibrator/main.nf b/tests/modules/nf-core/gatk4/baserecalibrator/main.nf index 19df0d65001..e66f2c0e45d 100644 --- a/tests/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/tests/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_BASERECALIBRATOR } from '../../../../modules/nf-core/gatk4/baserecalibrator/main.nf' +include { GATK4_BASERECALIBRATOR } from '../../../../../modules/nf-core/gatk4/baserecalibrator/main.nf' workflow test_gatk4_baserecalibrator { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf index e1d03c47d44..8108332ef7e 100644 --- a/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_BASERECALIBRATOR_SPARK } from '../../../../modules/nf-core/gatk4/baserecalibratorspark/main.nf' +include { GATK4_BASERECALIBRATOR_SPARK } from '../../../../../modules/nf-core/gatk4/baserecalibratorspark/main.nf' workflow test_gatk4_baserecalibrator_spark { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/main.nf b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf index c2414d4f1f6..3ee8478c870 100644 --- a/tests/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' +include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' workflow test_gatk4_bedtointervallist { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/main.nf b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf index a4ff1099e3b..dd24f2e055b 100644 --- a/tests/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/nf-core/gatk4/calculatecontamination/main.nf' -include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../modules/nf-core/gatk4/calculatecontamination/main.nf' +include { GATK4_CALCULATECONTAMINATION } from '../../../../../modules/nf-core/gatk4/calculatecontamination/main.nf' +include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../../modules/nf-core/gatk4/calculatecontamination/main.nf' workflow test_gatk4_calculatecontamination_tumor_only { diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 54f7b44e7b9..de7307aae95 100644 --- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../modules/nf-core/gatk4/calibratedragstrmodel/main.nf' +include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../../modules/nf-core/gatk4/calibratedragstrmodel/main.nf' workflow test_gatk4_calibratedragstrmodel_bam { diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf index c9b570dbac6..8a218e1b884 100644 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' +include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' workflow test_gatk4_cnnscorevariants { diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf index 08dfb5b1570..8a056a24c43 100644 --- a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COLLECTREADCOUNTS } from '../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' +include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' workflow test_gatk4_collectreadcounts_hdf5 { diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf index 277fc7215c3..68f406bd560 100644 --- a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' +include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' workflow test_gatk4_collectsvevidence_cram { diff --git a/tests/modules/nf-core/gatk4/combinegvcfs/main.nf b/tests/modules/nf-core/gatk4/combinegvcfs/main.nf index a518e050e50..42a92c9bef5 100644 --- a/tests/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/tests/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COMBINEGVCFS } from '../../../../modules/nf-core/gatk4/combinegvcfs/main.nf' +include { GATK4_COMBINEGVCFS } from '../../../../../modules/nf-core/gatk4/combinegvcfs/main.nf' workflow test_gatk4_combinegvcfs { diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf index e35032b7784..4c62f05de88 100644 --- a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/nf-core/gatk4/composestrtablefile/main.nf' +include { GATK4_COMPOSESTRTABLEFILE } from '../../../../../modules/nf-core/gatk4/composestrtablefile/main.nf' workflow test_gatk4_composestrtablefile { diff --git a/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf b/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf index 5398588422e..c687c15ec48 100644 --- a/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/tests/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../modules/nf-core/gatk4/createsequencedictionary/main.nf' +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../../modules/nf-core/gatk4/createsequencedictionary/main.nf' workflow test_gatk4_createsequencedictionary { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index df266647ca3..25a191d82ec 100644 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf' workflow test_gatk4_createsomaticpanelofnormals { db = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index d3458a904b2..decc9114132 100644 --- a/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/tests/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf' +include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf' workflow test_gatk4_estimatelibrarycomplexity { diff --git a/tests/modules/nf-core/gatk4/fastqtosam/main.nf b/tests/modules/nf-core/gatk4/fastqtosam/main.nf index 77a12aef9b0..0a3aef644d4 100644 --- a/tests/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/tests/modules/nf-core/gatk4/fastqtosam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_FASTQTOSAM } from '../../../../modules/nf-core/gatk4/fastqtosam/main.nf' +include { GATK4_FASTQTOSAM } from '../../../../../modules/nf-core/gatk4/fastqtosam/main.nf' workflow test_gatk4_fastqtosam_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf b/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf index da3e573fddc..039a39853d0 100644 --- a/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/tests/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/nf-core/gatk4/filtermutectcalls/main.nf' +include { GATK4_FILTERMUTECTCALLS } from '../../../../../modules/nf-core/gatk4/filtermutectcalls/main.nf' workflow test_gatk4_filtermutectcalls_base { diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf index bfb4e20ab54..5b2b0d484b3 100644 --- a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/nf-core/gatk4/filtervarianttranches/main.nf' -include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' -include { GATK4_HAPLOTYPECALLER } from '../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' +include { GATK4_FILTERVARIANTTRANCHES } from '../../../../../modules/nf-core/gatk4/filtervarianttranches/main.nf' +include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' +include { GATK4_HAPLOTYPECALLER } from '../../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' workflow test_gatk4_filtervarianttranches { resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 586008a5b1c..150c958c682 100644 --- a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_GATHERBQSRREPORTS } from '../../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf' +include { GATK4_GATHERBQSRREPORTS } from '../../../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf' workflow test_gatk4_gatherbqsrreports { diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index afe8dc39477..a30364439f5 100644 --- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../modules/nf-core/gatk4/gatherpileupsummaries/main.nf' +include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../../modules/nf-core/gatk4/gatherpileupsummaries/main.nf' workflow test_gatk4_gatherpileupsummaries { diff --git a/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf b/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf index 01fda733d2e..ca0b67241b9 100644 --- a/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/tests/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { GATK4_GENOMICSDBIMPORT } from '../../../../modules/nf-core/gatk4/genomicsdbimport/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { GATK4_GENOMICSDBIMPORT } from '../../../../../modules/nf-core/gatk4/genomicsdbimport/main.nf' workflow test_gatk4_genomicsdbimport_create_genomicsdb { diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf index b9b9a68a8bb..06423b29d1d 100644 --- a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_GENOTYPEGVCFS } from '../../../../modules/nf-core/gatk4/genotypegvcfs/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { GATK4_GENOTYPEGVCFS } from '../../../../../modules/nf-core/gatk4/genotypegvcfs/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' // Basic parameters with uncompressed VCF input workflow test_gatk4_genotypegvcfs_vcf_input { diff --git a/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf index 898d0e3b8b2..45a7cc116b7 100644 --- a/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/tests/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/nf-core/gatk4/getpileupsummaries/main.nf' +include { GATK4_GETPILEUPSUMMARIES } from '../../../../../modules/nf-core/gatk4/getpileupsummaries/main.nf' workflow test_gatk4_getpileupsummaries_separate_sites { diff --git a/tests/modules/nf-core/gatk4/haplotypecaller/main.nf b/tests/modules/nf-core/gatk4/haplotypecaller/main.nf index adee2d1a069..ada5013dda5 100644 --- a/tests/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/tests/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_HAPLOTYPECALLER } from '../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' +include { GATK4_HAPLOTYPECALLER } from '../../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' workflow test_gatk4_haplotypecaller { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf b/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf index 9e718295022..15c88cb38bb 100644 --- a/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/tests/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_INDEXFEATUREFILE } from '../../../../modules/nf-core/gatk4/indexfeaturefile/main.nf' +include { GATK4_INDEXFEATUREFILE } from '../../../../../modules/nf-core/gatk4/indexfeaturefile/main.nf' workflow test_gatk4_indexfeaturefile_bed { diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf index 81988b0bad8..c8a5b819098 100644 --- a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_INTERVALLISTTOBED } from '../../../../modules/nf-core/gatk4/intervallisttobed/main.nf' +include { GATK4_INTERVALLISTTOBED } from '../../../../../modules/nf-core/gatk4/intervallisttobed/main.nf' workflow test_gatk4_intervallisttobed { diff --git a/tests/modules/nf-core/gatk4/intervallisttools/main.nf b/tests/modules/nf-core/gatk4/intervallisttools/main.nf index 0239edbdf5f..0845c7d017d 100644 --- a/tests/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/tests/modules/nf-core/gatk4/intervallisttools/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' -include { GATK4_INTERVALLISTTOOLS } from '../../../../modules/nf-core/gatk4/intervallisttools/main.nf' +include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' +include { GATK4_INTERVALLISTTOOLS } from '../../../../../modules/nf-core/gatk4/intervallisttools/main.nf' workflow test_gatk4_intervallisttools { diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index efdf1e83262..5960a568964 100644 --- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/nf-core/gatk4/learnreadorientationmodel/main.nf' +include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../../modules/nf-core/gatk4/learnreadorientationmodel/main.nf' workflow test_gatk4_learnreadorientationmodel { diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index 192872cdb42..8028168f366 100644 --- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/nf-core/gatk4/leftalignandtrimvariants/main.nf' +include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../../modules/nf-core/gatk4/leftalignandtrimvariants/main.nf' workflow test_gatk4_leftalignandtrimvariants_interval { diff --git a/tests/modules/nf-core/gatk4/markduplicates/main.nf b/tests/modules/nf-core/gatk4/markduplicates/main.nf index c76813c3e36..90d7402684f 100644 --- a/tests/modules/nf-core/gatk4/markduplicates/main.nf +++ b/tests/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_MARKDUPLICATES } from '../../../../modules/nf-core/gatk4/markduplicates/main.nf' -include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/nf-core/gatk4/markduplicates/main.nf' +include { GATK4_MARKDUPLICATES } from '../../../../../modules/nf-core/gatk4/markduplicates/main.nf' +include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../../modules/nf-core/gatk4/markduplicates/main.nf' workflow test_gatk4_markduplicates { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf b/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf index 64e4261bcda..e2fe9f7f8fa 100644 --- a/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/tests/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' -include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' -include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' +include { GATK4_MARKDUPLICATES_SPARK } from '../../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' +include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' +include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../../modules/nf-core/gatk4/markduplicatesspark/main.nf' workflow test_gatk4_markduplicates_spark { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf index da2fc14444a..6c5d463534f 100644 --- a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/nf-core/gatk4/mergebamalignment/main.nf' +include { GATK4_MERGEBAMALIGNMENT } from '../../../../../modules/nf-core/gatk4/mergebamalignment/main.nf' workflow test_gatk4_mergebamalignment { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/mergemutectstats/main.nf b/tests/modules/nf-core/gatk4/mergemutectstats/main.nf index 522f48c2142..672706ad3cf 100644 --- a/tests/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/tests/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_MERGEMUTECTSTATS } from '../../../../modules/nf-core/gatk4/mergemutectstats/main.nf' +include { GATK4_MERGEMUTECTSTATS } from '../../../../../modules/nf-core/gatk4/mergemutectstats/main.nf' workflow test_gatk4_mergemutectstats { diff --git a/tests/modules/nf-core/gatk4/mergevcfs/main.nf b/tests/modules/nf-core/gatk4/mergevcfs/main.nf index e10575e9429..0316fc441eb 100644 --- a/tests/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/tests/modules/nf-core/gatk4/mergevcfs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_MERGEVCFS } from '../../../../modules/nf-core/gatk4/mergevcfs/main.nf' +include { GATK4_MERGEVCFS } from '../../../../../modules/nf-core/gatk4/mergevcfs/main.nf' workflow test_gatk4_mergevcfs { def input = [] diff --git a/tests/modules/nf-core/gatk4/mutect2/main.nf b/tests/modules/nf-core/gatk4/mutect2/main.nf index 6385c51dfec..7567f7cebc8 100644 --- a/tests/modules/nf-core/gatk4/mutect2/main.nf +++ b/tests/modules/nf-core/gatk4/mutect2/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GATK4_MUTECT2 } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' -include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' -include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' -include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 as GATK4_MUTECT2_PAIR } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 as GATK4_MUTECT2_MITO } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf' +include { GATK4_MUTECT2 as GATK4_MUTECT2_F1R2 } from '../../../../../modules/nf-core/gatk4/mutect2/main.nf' workflow test_gatk4_mutect2_tumor_normal_pair { input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map diff --git a/tests/modules/nf-core/gatk4/printsvevidence/main.nf b/tests/modules/nf-core/gatk4/printsvevidence/main.nf index 2389046e770..78bf31cdaf4 100644 --- a/tests/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/tests/modules/nf-core/gatk4/printsvevidence/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../modules/nf-core/gatk4/printsvevidence/main.nf' -include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../modules/nf-core/gatk4/printsvevidence/main.nf' -include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' +include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../../modules/nf-core/gatk4/printsvevidence/main.nf' +include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../../modules/nf-core/gatk4/printsvevidence/main.nf' +include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' workflow test_gatk4_printsvevidence { diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/main.nf b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf index 5e8c7dc7780..d379e8fd828 100644 --- a/tests/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_REBLOCKGVCF } from '../../../../modules/nf-core/gatk4/reblockgvcf/main.nf' +include { GATK4_REBLOCKGVCF } from '../../../../../modules/nf-core/gatk4/reblockgvcf/main.nf' workflow test_gatk4_reblockgvcf { diff --git a/tests/modules/nf-core/gatk4/revertsam/main.nf b/tests/modules/nf-core/gatk4/revertsam/main.nf index 3a6a8ad3e10..2f4c153be69 100644 --- a/tests/modules/nf-core/gatk4/revertsam/main.nf +++ b/tests/modules/nf-core/gatk4/revertsam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_REVERTSAM } from '../../../../modules/nf-core/gatk4/revertsam/main.nf' +include { GATK4_REVERTSAM } from '../../../../../modules/nf-core/gatk4/revertsam/main.nf' workflow test_gatk4_revertsam { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/samtofastq/main.nf b/tests/modules/nf-core/gatk4/samtofastq/main.nf index 6ec4b4c8194..35f1f9d36c9 100644 --- a/tests/modules/nf-core/gatk4/samtofastq/main.nf +++ b/tests/modules/nf-core/gatk4/samtofastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SAMTOFASTQ } from '../../../../modules/nf-core/gatk4/samtofastq/main.nf' +include { GATK4_SAMTOFASTQ } from '../../../../../modules/nf-core/gatk4/samtofastq/main.nf' workflow test_gatk4_samtofastq_single_end { input = [ [ id:'test', single_end: true ], // meta map diff --git a/tests/modules/nf-core/gatk4/selectvariants/main.nf b/tests/modules/nf-core/gatk4/selectvariants/main.nf index 047ef8def10..5ded13562a7 100644 --- a/tests/modules/nf-core/gatk4/selectvariants/main.nf +++ b/tests/modules/nf-core/gatk4/selectvariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SELECTVARIANTS } from '../../../../modules/nf-core/gatk4/selectvariants/main.nf' +include { GATK4_SELECTVARIANTS } from '../../../../../modules/nf-core/gatk4/selectvariants/main.nf' // Basic parameters with uncompressed VCF input workflow test_gatk4_selectvariants_vcf_input { diff --git a/tests/modules/nf-core/gatk4/splitintervals/main.nf b/tests/modules/nf-core/gatk4/splitintervals/main.nf index 7c73ee18f32..5c744e351ce 100644 --- a/tests/modules/nf-core/gatk4/splitintervals/main.nf +++ b/tests/modules/nf-core/gatk4/splitintervals/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SPLITINTERVALS } from '../../../../modules/nf-core/gatk4/splitintervals/main.nf' +include { GATK4_SPLITINTERVALS } from '../../../../../modules/nf-core/gatk4/splitintervals/main.nf' workflow test_gatk4_splitintervals_bed { diff --git a/tests/modules/nf-core/gatk4/splitncigarreads/main.nf b/tests/modules/nf-core/gatk4/splitncigarreads/main.nf index 64e62a49d08..979cf8b9a90 100644 --- a/tests/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/tests/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_SPLITNCIGARREADS } from '../../../../modules/nf-core/gatk4/splitncigarreads/main.nf' +include { GATK4_SPLITNCIGARREADS } from '../../../../../modules/nf-core/gatk4/splitncigarreads/main.nf' workflow test_gatk4_splitncigarreads { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gatk4/variantfiltration/main.nf b/tests/modules/nf-core/gatk4/variantfiltration/main.nf index 8ec45813d8c..0b90440740a 100644 --- a/tests/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/tests/modules/nf-core/gatk4/variantfiltration/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GATK4_VARIANTFILTRATION } from '../../../../modules/nf-core/gatk4/variantfiltration/main.nf' +include { GATK4_VARIANTFILTRATION } from '../../../../../modules/nf-core/gatk4/variantfiltration/main.nf' // Basic parameters with uncompressed VCF input workflow test_gatk4_variantfiltration_vcf_input { diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf index a492ae2f9f7..f8680f9dec1 100644 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' workflow test_gatk4_variantrecalibrator { diff --git a/tests/modules/nf-core/gecco/run/main.nf b/tests/modules/nf-core/gecco/run/main.nf index 01f320df609..76b971e2ffa 100644 --- a/tests/modules/nf-core/gecco/run/main.nf +++ b/tests/modules/nf-core/gecco/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GECCO_RUN } from '../../../../modules/nf-core/gecco/run/main.nf' +include { GECCO_RUN } from '../../../../../modules/nf-core/gecco/run/main.nf' workflow test_gecco_run { diff --git a/tests/modules/nf-core/genescopefk/main.nf b/tests/modules/nf-core/genescopefk/main.nf index 72f10e566e9..fcd2fc491a5 100644 --- a/tests/modules/nf-core/genescopefk/main.nf +++ b/tests/modules/nf-core/genescopefk/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../modules/nf-core/fastk/fastk/main.nf' -include { FASTK_HISTEX } from '../../../modules/nf-core/fastk/histex/main.nf' -include { GENESCOPEFK } from '../../../modules/nf-core/genescopefk/main.nf' +include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_HISTEX } from '../../../../modules/nf-core/fastk/histex/main.nf' +include { GENESCOPEFK } from '../../../../modules/nf-core/genescopefk/main.nf' workflow test_genescopefk { diff --git a/tests/modules/nf-core/genmap/index/main.nf b/tests/modules/nf-core/genmap/index/main.nf index db7f85b3407..1135eb977c6 100644 --- a/tests/modules/nf-core/genmap/index/main.nf +++ b/tests/modules/nf-core/genmap/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMAP_INDEX } from '../../../../modules/nf-core/genmap/index/main.nf' +include { GENMAP_INDEX } from '../../../../../modules/nf-core/genmap/index/main.nf' workflow test_genmap_index { diff --git a/tests/modules/nf-core/genmap/mappability/main.nf b/tests/modules/nf-core/genmap/mappability/main.nf index aed4ed73bb9..ba2e996e93b 100644 --- a/tests/modules/nf-core/genmap/mappability/main.nf +++ b/tests/modules/nf-core/genmap/mappability/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GENMAP_INDEX } from '../../../../modules/nf-core/genmap/index/main.nf' -include { GENMAP_MAPPABILITY } from '../../../../modules/nf-core/genmap/mappability/main.nf' +include { GENMAP_INDEX } from '../../../../../modules/nf-core/genmap/index/main.nf' +include { GENMAP_MAPPABILITY } from '../../../../../modules/nf-core/genmap/mappability/main.nf' workflow test_genmap_map { diff --git a/tests/modules/nf-core/genmod/annotate/main.nf b/tests/modules/nf-core/genmod/annotate/main.nf index d2a6190ae92..5152245453f 100644 --- a/tests/modules/nf-core/genmod/annotate/main.nf +++ b/tests/modules/nf-core/genmod/annotate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_ANNOTATE } from '../../../../modules/nf-core/genmod/annotate/main.nf' +include { GENMOD_ANNOTATE } from '../../../../../modules/nf-core/genmod/annotate/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genmod/compound/main.nf b/tests/modules/nf-core/genmod/compound/main.nf index fa817d412a2..ce0bb4779d2 100644 --- a/tests/modules/nf-core/genmod/compound/main.nf +++ b/tests/modules/nf-core/genmod/compound/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_COMPOUND } from '../../../../modules/nf-core/genmod/compound/main.nf' +include { GENMOD_COMPOUND } from '../../../../../modules/nf-core/genmod/compound/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genmod/models/main.nf b/tests/modules/nf-core/genmod/models/main.nf index a7434557615..ef983c48dc9 100644 --- a/tests/modules/nf-core/genmod/models/main.nf +++ b/tests/modules/nf-core/genmod/models/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_MODELS } from '../../../../modules/nf-core/genmod/models/main.nf' +include { GENMOD_MODELS } from '../../../../../modules/nf-core/genmod/models/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genmod/score/main.nf b/tests/modules/nf-core/genmod/score/main.nf index 5929ff475c7..d7c8c5c1a08 100644 --- a/tests/modules/nf-core/genmod/score/main.nf +++ b/tests/modules/nf-core/genmod/score/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GENMOD_SCORE } from '../../../../modules/nf-core/genmod/score/main.nf' +include { GENMOD_SCORE } from '../../../../../modules/nf-core/genmod/score/main.nf' input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/genomescope2/main.nf b/tests/modules/nf-core/genomescope2/main.nf index b56b798fe91..1cb7c1b2229 100644 --- a/tests/modules/nf-core/genomescope2/main.nf +++ b/tests/modules/nf-core/genomescope2/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../modules/nf-core/meryl/count/main.nf' -include { MERYL_HISTOGRAM } from '../../../modules/nf-core/meryl/histogram/main.nf' -include { GENOMESCOPE2 } from '../../../modules/nf-core/genomescope2/main.nf' +include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_HISTOGRAM } from '../../../../modules/nf-core/meryl/histogram/main.nf' +include { GENOMESCOPE2 } from '../../../../modules/nf-core/genomescope2/main.nf' workflow test_genomescope2 { diff --git a/tests/modules/nf-core/genotyphi/parse/main.nf b/tests/modules/nf-core/genotyphi/parse/main.nf index 9eca9afee50..6e5f633ec1b 100644 --- a/tests/modules/nf-core/genotyphi/parse/main.nf +++ b/tests/modules/nf-core/genotyphi/parse/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MYKROBE_PREDICT } from '../../../../modules/nf-core/mykrobe/predict/main.nf' -include { GENOTYPHI_PARSE } from '../../../../modules/nf-core/genotyphi/parse/main.nf' +include { MYKROBE_PREDICT } from '../../../../../modules/nf-core/mykrobe/predict/main.nf' +include { GENOTYPHI_PARSE } from '../../../../../modules/nf-core/genotyphi/parse/main.nf' workflow test_mykrobe_predict { diff --git a/tests/modules/nf-core/genrich/main.nf b/tests/modules/nf-core/genrich/main.nf index e7f9d5829ea..71f9b21ccbe 100644 --- a/tests/modules/nf-core/genrich/main.nf +++ b/tests/modules/nf-core/genrich/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GENRICH } from '../../../modules/nf-core/genrich/main.nf' -include { GENRICH as GENRICH_CTRL } from '../../../modules/nf-core/genrich/main.nf' -include { GENRICH as GENRICH_ALL } from '../../../modules/nf-core/genrich/main.nf' -include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/nf-core/genrich/main.nf' +include { GENRICH } from '../../../../modules/nf-core/genrich/main.nf' +include { GENRICH as GENRICH_CTRL } from '../../../../modules/nf-core/genrich/main.nf' +include { GENRICH as GENRICH_ALL } from '../../../../modules/nf-core/genrich/main.nf' +include { GENRICH as GENRICH_ATACSEQ } from '../../../../modules/nf-core/genrich/main.nf' workflow test_genrich { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/gfaffix/main.nf b/tests/modules/nf-core/gfaffix/main.nf index 43b833a418c..712f7dca3e1 100644 --- a/tests/modules/nf-core/gfaffix/main.nf +++ b/tests/modules/nf-core/gfaffix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GFAFFIX } from '../../../modules/nf-core/gfaffix/main.nf' +include { GFAFFIX } from '../../../../modules/nf-core/gfaffix/main.nf' workflow test_gfaffix { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/gffread/main.nf b/tests/modules/nf-core/gffread/main.nf index 5a3f2185765..014f938a518 100644 --- a/tests/modules/nf-core/gffread/main.nf +++ b/tests/modules/nf-core/gffread/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GFFREAD } from '../../../modules/nf-core/gffread/main.nf' +include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' workflow test_gffread { input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) diff --git a/tests/modules/nf-core/glimpse/chunk/main.nf b/tests/modules/nf-core/glimpse/chunk/main.nf index c716ff35f67..594d3e0d7b6 100644 --- a/tests/modules/nf-core/glimpse/chunk/main.nf +++ b/tests/modules/nf-core/glimpse/chunk/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GLIMPSE_CHUNK } from '../../../../modules/nf-core/glimpse/chunk/main.nf' +include { GLIMPSE_CHUNK } from '../../../../../modules/nf-core/glimpse/chunk/main.nf' workflow test_glimpse_chunk { input = [ diff --git a/tests/modules/nf-core/glnexus/main.nf b/tests/modules/nf-core/glnexus/main.nf index a85d8b37926..86debecc4ab 100644 --- a/tests/modules/nf-core/glnexus/main.nf +++ b/tests/modules/nf-core/glnexus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GLNEXUS } from '../../../modules/nf-core/glnexus/main.nf' +include { GLNEXUS } from '../../../../modules/nf-core/glnexus/main.nf' workflow test_glnexus { input = [ diff --git a/tests/modules/nf-core/goat/taxonsearch/main.nf b/tests/modules/nf-core/goat/taxonsearch/main.nf index a58c9b24e55..cc8db9235d6 100644 --- a/tests/modules/nf-core/goat/taxonsearch/main.nf +++ b/tests/modules/nf-core/goat/taxonsearch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GOAT_TAXONSEARCH } from '../../../../modules/nf-core/goat/taxonsearch/main.nf' +include { GOAT_TAXONSEARCH } from '../../../../../modules/nf-core/goat/taxonsearch/main.nf' // // Test with genus name (Canis) diff --git a/tests/modules/nf-core/graphmap2/align/main.nf b/tests/modules/nf-core/graphmap2/align/main.nf index fa44b8b2eae..d4dc83d9d39 100644 --- a/tests/modules/nf-core/graphmap2/align/main.nf +++ b/tests/modules/nf-core/graphmap2/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GRAPHMAP2_INDEX } from '../../../../modules/nf-core/graphmap2/index/main.nf' -include { GRAPHMAP2_ALIGN } from '../../../../modules/nf-core/graphmap2/align/main.nf' +include { GRAPHMAP2_INDEX } from '../../../../../modules/nf-core/graphmap2/index/main.nf' +include { GRAPHMAP2_ALIGN } from '../../../../../modules/nf-core/graphmap2/align/main.nf' workflow test_graphmap2_align { diff --git a/tests/modules/nf-core/graphmap2/index/main.nf b/tests/modules/nf-core/graphmap2/index/main.nf index b382ec4d96d..cb71cd9918a 100644 --- a/tests/modules/nf-core/graphmap2/index/main.nf +++ b/tests/modules/nf-core/graphmap2/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GRAPHMAP2_INDEX } from '../../../../modules/nf-core/graphmap2/index/main.nf' +include { GRAPHMAP2_INDEX } from '../../../../../modules/nf-core/graphmap2/index/main.nf' workflow test_graphmap2_index { diff --git a/tests/modules/nf-core/gstama/collapse/main.nf b/tests/modules/nf-core/gstama/collapse/main.nf index 054518729d0..20c3ff74ccf 100644 --- a/tests/modules/nf-core/gstama/collapse/main.nf +++ b/tests/modules/nf-core/gstama/collapse/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GSTAMA_COLLAPSE } from '../../../../modules/nf-core/gstama/collapse/main.nf' +include { GSTAMA_COLLAPSE } from '../../../../../modules/nf-core/gstama/collapse/main.nf' workflow test_gstama_collapse { diff --git a/tests/modules/nf-core/gstama/merge/main.nf b/tests/modules/nf-core/gstama/merge/main.nf index a892e23e3aa..dad081f557b 100644 --- a/tests/modules/nf-core/gstama/merge/main.nf +++ b/tests/modules/nf-core/gstama/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GSTAMA_MERGE } from '../../../../modules/nf-core/gstama/merge/main' +include { GSTAMA_MERGE } from '../../../../../modules/nf-core/gstama/merge/main' workflow test_gstama_merge { diff --git a/tests/modules/nf-core/gstama/polyacleanup/main.nf b/tests/modules/nf-core/gstama/polyacleanup/main.nf index de05947db94..e1ed59663f9 100644 --- a/tests/modules/nf-core/gstama/polyacleanup/main.nf +++ b/tests/modules/nf-core/gstama/polyacleanup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GSTAMA_POLYACLEANUP } from '../../../../modules/nf-core/gstama/polyacleanup/main.nf' +include { GSTAMA_POLYACLEANUP } from '../../../../../modules/nf-core/gstama/polyacleanup/main.nf' workflow test_gstama_polyacleanup { diff --git a/tests/modules/nf-core/gtdbtk/classifywf/main.nf b/tests/modules/nf-core/gtdbtk/classifywf/main.nf index f84a8b2f789..a3373a1e9b9 100644 --- a/tests/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/tests/modules/nf-core/gtdbtk/classifywf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GTDBTK_CLASSIFYWF } from '../../../../modules/nf-core/gtdbtk/classifywf/main.nf' +include { GTDBTK_CLASSIFYWF } from '../../../../../modules/nf-core/gtdbtk/classifywf/main.nf' process STUB_GTDBTK_DATABASE { output: diff --git a/tests/modules/nf-core/gubbins/main.nf b/tests/modules/nf-core/gubbins/main.nf index 74993ac943e..f65460d821e 100644 --- a/tests/modules/nf-core/gubbins/main.nf +++ b/tests/modules/nf-core/gubbins/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GUBBINS } from '../../../modules/nf-core/gubbins/main.nf' +include { GUBBINS } from '../../../../modules/nf-core/gubbins/main.nf' workflow test_gubbins { input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true) diff --git a/tests/modules/nf-core/gunc/downloaddb/main.nf b/tests/modules/nf-core/gunc/downloaddb/main.nf index 0861a9111bc..a708f54e6ff 100644 --- a/tests/modules/nf-core/gunc/downloaddb/main.nf +++ b/tests/modules/nf-core/gunc/downloaddb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GUNC_DOWNLOADDB } from '../../../../modules/nf-core/gunc/downloaddb/main.nf' +include { GUNC_DOWNLOADDB } from '../../../../../modules/nf-core/gunc/downloaddb/main.nf' workflow test_gunc_downloaddb { diff --git a/tests/modules/nf-core/gunc/run/main.nf b/tests/modules/nf-core/gunc/run/main.nf index f7a10825fc2..b676599ec38 100644 --- a/tests/modules/nf-core/gunc/run/main.nf +++ b/tests/modules/nf-core/gunc/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { GUNC_RUN } from '../../../../modules/nf-core/gunc/run/main.nf' -include { GUNC_DOWNLOADDB } from '../../../../modules/nf-core/gunc/downloaddb/main.nf' +include { GUNC_RUN } from '../../../../../modules/nf-core/gunc/run/main.nf' +include { GUNC_DOWNLOADDB } from '../../../../../modules/nf-core/gunc/downloaddb/main.nf' workflow test_gunc_run { diff --git a/tests/modules/nf-core/gunzip/main.nf b/tests/modules/nf-core/gunzip/main.nf index 1a1af3b5ca2..b106b1e6ac1 100644 --- a/tests/modules/nf-core/gunzip/main.nf +++ b/tests/modules/nf-core/gunzip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' workflow test_gunzip { input = [ [], diff --git a/tests/modules/nf-core/gvcftools/extractvariants/main.nf b/tests/modules/nf-core/gvcftools/extractvariants/main.nf index acad43faf16..0d26f24e5f5 100644 --- a/tests/modules/nf-core/gvcftools/extractvariants/main.nf +++ b/tests/modules/nf-core/gvcftools/extractvariants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { GVCFTOOLS_EXTRACTVARIANTS } from '../../../../modules/nf-core/gvcftools/extractvariants/main.nf' +include { GVCFTOOLS_EXTRACTVARIANTS } from '../../../../../modules/nf-core/gvcftools/extractvariants/main.nf' workflow test_gvcftools_extractvariants { diff --git a/tests/modules/nf-core/hamronization/abricate/main.nf b/tests/modules/nf-core/hamronization/abricate/main.nf index aeb667de1b1..51fbf61ad5a 100644 --- a/tests/modules/nf-core/hamronization/abricate/main.nf +++ b/tests/modules/nf-core/hamronization/abricate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAMRONIZATION_ABRICATE } from '../../../../modules/nf-core/hamronization/abricate/main.nf' +include { HAMRONIZATION_ABRICATE } from '../../../../../modules/nf-core/hamronization/abricate/main.nf' workflow test_hamronization_abricate { diff --git a/tests/modules/nf-core/hamronization/amrfinderplus/main.nf b/tests/modules/nf-core/hamronization/amrfinderplus/main.nf index e63cc558173..2410104ce3d 100644 --- a/tests/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/tests/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../modules/nf-core/hamronization/amrfinderplus/main.nf' +include { HAMRONIZATION_AMRFINDERPLUS } from '../../../../../modules/nf-core/hamronization/amrfinderplus/main.nf' workflow test_hamronization_amrfinderplus { diff --git a/tests/modules/nf-core/hamronization/deeparg/main.nf b/tests/modules/nf-core/hamronization/deeparg/main.nf index 6f4f196069e..ad452e0d415 100644 --- a/tests/modules/nf-core/hamronization/deeparg/main.nf +++ b/tests/modules/nf-core/hamronization/deeparg/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAMRONIZATION_DEEPARG } from '../../../../modules/nf-core/hamronization/deeparg/main.nf' +include { HAMRONIZATION_DEEPARG } from '../../../../../modules/nf-core/hamronization/deeparg/main.nf' workflow test_hamronization_deeparg { diff --git a/tests/modules/nf-core/hamronization/fargene/main.nf b/tests/modules/nf-core/hamronization/fargene/main.nf index 599585ea2f9..6ded7b2ac34 100644 --- a/tests/modules/nf-core/hamronization/fargene/main.nf +++ b/tests/modules/nf-core/hamronization/fargene/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' -include { FARGENE } from '../../../modules/nf-core/fargene/main.nf' -include { HAMRONIZATION_FARGENE } from '../../../../modules/nf-core/hamronization/fargene/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { FARGENE } from '../../../../modules/nf-core/fargene/main.nf' +include { HAMRONIZATION_FARGENE } from '../../../../../modules/nf-core/hamronization/fargene/main.nf' workflow test_hamronization_fargene { diff --git a/tests/modules/nf-core/hamronization/rgi/main.nf b/tests/modules/nf-core/hamronization/rgi/main.nf index 4407d0f9cd2..ef9c5a9fd89 100644 --- a/tests/modules/nf-core/hamronization/rgi/main.nf +++ b/tests/modules/nf-core/hamronization/rgi/main.nf @@ -1,8 +1,8 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -include { RGI_MAIN } from '../../../../modules/nf-core/rgi/main/main.nf' -include { HAMRONIZATION_RGI } from '../../../../modules/nf-core/hamronization/rgi/main.nf' +include { RGI_MAIN } from '../../../../../modules/nf-core/rgi/main/main.nf' +include { HAMRONIZATION_RGI } from '../../../../../modules/nf-core/hamronization/rgi/main.nf' workflow test_hamronization_rgi { diff --git a/tests/modules/nf-core/hamronization/summarize/main.nf b/tests/modules/nf-core/hamronization/summarize/main.nf index 67f57675352..b5f096c0b13 100644 --- a/tests/modules/nf-core/hamronization/summarize/main.nf +++ b/tests/modules/nf-core/hamronization/summarize/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { HAMRONIZATION_DEEPARG } from '../../../../modules/nf-core/hamronization/deeparg/main.nf' -include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/nf-core/hamronization/deeparg/main.nf' -include { HAMRONIZATION_SUMMARIZE } from '../../../../modules/nf-core/hamronization/summarize/main.nf' +include { HAMRONIZATION_DEEPARG } from '../../../../../modules/nf-core/hamronization/deeparg/main.nf' +include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../../modules/nf-core/hamronization/deeparg/main.nf' +include { HAMRONIZATION_SUMMARIZE } from '../../../../../modules/nf-core/hamronization/summarize/main.nf' workflow test_hamronization_summarize { diff --git a/tests/modules/nf-core/haplocheck/main.nf b/tests/modules/nf-core/haplocheck/main.nf index cde2586ba14..b00de96ff49 100644 --- a/tests/modules/nf-core/haplocheck/main.nf +++ b/tests/modules/nf-core/haplocheck/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPLOCHECK } from '../../../modules/nf-core/haplocheck/main.nf' +include { HAPLOCHECK } from '../../../../modules/nf-core/haplocheck/main.nf' workflow test_haplocheck { diff --git a/tests/modules/nf-core/haplogrep2/classify/main.nf b/tests/modules/nf-core/haplogrep2/classify/main.nf index ebb844863fb..6385aed5de7 100644 --- a/tests/modules/nf-core/haplogrep2/classify/main.nf +++ b/tests/modules/nf-core/haplogrep2/classify/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPLOGREP2_CLASSIFY } from '../../../../modules/nf-core/haplogrep2/classify/main.nf' +include { HAPLOGREP2_CLASSIFY } from '../../../../../modules/nf-core/haplogrep2/classify/main.nf' workflow test_haplogrep2_classify { diff --git a/tests/modules/nf-core/happy/happy/main.nf b/tests/modules/nf-core/happy/happy/main.nf index e31511197ed..0b6f898fc7a 100644 --- a/tests/modules/nf-core/happy/happy/main.nf +++ b/tests/modules/nf-core/happy/happy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPPY_HAPPY } from '../../../../modules/nf-core/happy/happy/main.nf' +include { HAPPY_HAPPY } from '../../../../../modules/nf-core/happy/happy/main.nf' workflow test_happy_vcf { diff --git a/tests/modules/nf-core/happy/prepy/main.nf b/tests/modules/nf-core/happy/prepy/main.nf index d3f9b63f123..2991b1d1220 100644 --- a/tests/modules/nf-core/happy/prepy/main.nf +++ b/tests/modules/nf-core/happy/prepy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HAPPY_PREPY } from '../../../../modules/nf-core/happy/prepy/main.nf' +include { HAPPY_PREPY } from '../../../../../modules/nf-core/happy/prepy/main.nf' workflow test_happy_prepy_vcf { diff --git a/tests/modules/nf-core/hicap/main.nf b/tests/modules/nf-core/hicap/main.nf index 46e797534f3..b74a9656015 100644 --- a/tests/modules/nf-core/hicap/main.nf +++ b/tests/modules/nf-core/hicap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HICAP } from '../../../modules/nf-core/hicap/main.nf' +include { HICAP } from '../../../../modules/nf-core/hicap/main.nf' workflow test_hicap { diff --git a/tests/modules/nf-core/hifiasm/main.nf b/tests/modules/nf-core/hifiasm/main.nf index 1d4cb18e0f5..e52e91e99de 100644 --- a/tests/modules/nf-core/hifiasm/main.nf +++ b/tests/modules/nf-core/hifiasm/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HIFIASM } from '../../../modules/nf-core/hifiasm/main.nf' +include { HIFIASM } from '../../../../modules/nf-core/hifiasm/main.nf' /* * Test with long reads only diff --git a/tests/modules/nf-core/hisat2/align/main.nf b/tests/modules/nf-core/hisat2/align/main.nf index df406883400..2c0590842e4 100644 --- a/tests/modules/nf-core/hisat2/align/main.nf +++ b/tests/modules/nf-core/hisat2/align/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' -include { HISAT2_BUILD } from '../../../../modules/nf-core/hisat2/build/main.nf' -include { HISAT2_ALIGN } from '../../../../modules/nf-core/hisat2/align/main.nf' +include { HISAT2_EXTRACTSPLICESITES } from '../../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' +include { HISAT2_BUILD } from '../../../../../modules/nf-core/hisat2/build/main.nf' +include { HISAT2_ALIGN } from '../../../../../modules/nf-core/hisat2/align/main.nf' workflow test_hisat2_align_single_end { input = [ diff --git a/tests/modules/nf-core/hisat2/build_test/main.nf b/tests/modules/nf-core/hisat2/build_test/main.nf index f43bd8c6014..8029d10e2ff 100644 --- a/tests/modules/nf-core/hisat2/build_test/main.nf +++ b/tests/modules/nf-core/hisat2/build_test/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' -include { HISAT2_BUILD } from '../../../../modules/nf-core/hisat2/build/main.nf' +include { HISAT2_EXTRACTSPLICESITES } from '../../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' +include { HISAT2_BUILD } from '../../../../../modules/nf-core/hisat2/build/main.nf' workflow test_hisat2_build { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/hisat2/extractsplicesites/main.nf b/tests/modules/nf-core/hisat2/extractsplicesites/main.nf index a7203de85bc..0a05990af00 100644 --- a/tests/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/tests/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' +include { HISAT2_EXTRACTSPLICESITES } from '../../../../../modules/nf-core/hisat2/extractsplicesites/main.nf' workflow test_hisat2_extractsplicesites { gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) diff --git a/tests/modules/nf-core/hmmcopy/gccounter/main.nf b/tests/modules/nf-core/hmmcopy/gccounter/main.nf index 0b635a9b764..8ef200a92e3 100644 --- a/tests/modules/nf-core/hmmcopy/gccounter/main.nf +++ b/tests/modules/nf-core/hmmcopy/gccounter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_GCCOUNTER } from '../../../../modules/nf-core/hmmcopy/gccounter/main.nf' +include { HMMCOPY_GCCOUNTER } from '../../../../../modules/nf-core/hmmcopy/gccounter/main.nf' workflow test_hmmcopy_gccounter { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/hmmcopy/generatemap/main.nf b/tests/modules/nf-core/hmmcopy/generatemap/main.nf index 122b6b21722..e89f152571b 100644 --- a/tests/modules/nf-core/hmmcopy/generatemap/main.nf +++ b/tests/modules/nf-core/hmmcopy/generatemap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_GENERATEMAP } from '../../../../modules/nf-core/hmmcopy/generatemap/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../../modules/nf-core/hmmcopy/generatemap/main.nf' workflow test_hmmcopy_generatemap { diff --git a/tests/modules/nf-core/hmmcopy/mapcounter/main.nf b/tests/modules/nf-core/hmmcopy/mapcounter/main.nf index 11a8dffb64e..afc3cee2370 100644 --- a/tests/modules/nf-core/hmmcopy/mapcounter/main.nf +++ b/tests/modules/nf-core/hmmcopy/mapcounter/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_MAPCOUNTER } from '../../../../modules/nf-core/hmmcopy/mapcounter/main.nf' -include { HMMCOPY_GENERATEMAP } from '../../../../modules/nf-core/hmmcopy/generatemap/main.nf' +include { HMMCOPY_MAPCOUNTER } from '../../../../../modules/nf-core/hmmcopy/mapcounter/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../../modules/nf-core/hmmcopy/generatemap/main.nf' workflow test_hmmcopy_mapcounter { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/hmmcopy/readcounter/main.nf b/tests/modules/nf-core/hmmcopy/readcounter/main.nf index 7aa28ace0a9..03cda463d5b 100644 --- a/tests/modules/nf-core/hmmcopy/readcounter/main.nf +++ b/tests/modules/nf-core/hmmcopy/readcounter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMCOPY_READCOUNTER } from '../../../../modules/nf-core/hmmcopy/readcounter/main.nf' +include { HMMCOPY_READCOUNTER } from '../../../../../modules/nf-core/hmmcopy/readcounter/main.nf' workflow test_hmmcopy_readcounter { diff --git a/tests/modules/nf-core/hmmer/eslalimask/main.nf b/tests/modules/nf-core/hmmer/eslalimask/main.nf index 1213f09d956..c1a92a9ece8 100644 --- a/tests/modules/nf-core/hmmer/eslalimask/main.nf +++ b/tests/modules/nf-core/hmmer/eslalimask/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMALIGN } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' -include { HMMER_ESLALIMASK as RFMASK } from '../../../../modules/nf-core/hmmer/eslalimask/main.nf' +include { HMMER_HMMALIGN } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_ESLALIMASK as RFMASK } from '../../../../../modules/nf-core/hmmer/eslalimask/main.nf' workflow test_hmmer_rfmask { diff --git a/tests/modules/nf-core/hmmer/eslreformat/main.nf b/tests/modules/nf-core/hmmer/eslreformat/main.nf index bef217f544d..92f23eafa12 100644 --- a/tests/modules/nf-core/hmmer/eslreformat/main.nf +++ b/tests/modules/nf-core/hmmer/eslreformat/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMALIGN } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' -include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_AFA } from '../../../../modules/nf-core/hmmer/eslreformat/main.nf' -include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_PHYLIP } from '../../../../modules/nf-core/hmmer/eslreformat/main.nf' -include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_UNALIGN } from '../../../../modules/nf-core/hmmer/eslreformat/main.nf' +include { HMMER_HMMALIGN } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_AFA } from '../../../../../modules/nf-core/hmmer/eslreformat/main.nf' +include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_PHYLIP } from '../../../../../modules/nf-core/hmmer/eslreformat/main.nf' +include { HMMER_ESLREFORMAT as HMMER_ESLREFORMAT_UNALIGN } from '../../../../../modules/nf-core/hmmer/eslreformat/main.nf' workflow test_hmmer_eslreformat_afa { diff --git a/tests/modules/nf-core/hmmer/hmmalign/main.nf b/tests/modules/nf-core/hmmer/hmmalign/main.nf index e5d8e3b6c80..64814641c3d 100644 --- a/tests/modules/nf-core/hmmer/hmmalign/main.nf +++ b/tests/modules/nf-core/hmmer/hmmalign/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMALIGN as HMMER_HMMALIGN } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' -include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_HMMALIGN as HMMER_HMMALIGN } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf' +include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf' workflow test_hmmer_hmmalign { diff --git a/tests/modules/nf-core/hmmer/hmmbuild/main.nf b/tests/modules/nf-core/hmmer/hmmbuild/main.nf index dc4b0e8e6ab..7bd3a4b3a5f 100644 --- a/tests/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/tests/modules/nf-core/hmmer/hmmbuild/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMBUILD } from '../../../../modules/nf-core/hmmer/hmmbuild/main.nf' +include { HMMER_HMMBUILD } from '../../../../../modules/nf-core/hmmer/hmmbuild/main.nf' workflow test_hmmer_hmmbuild { diff --git a/tests/modules/nf-core/hmmer/hmmsearch/main.nf b/tests/modules/nf-core/hmmer/hmmsearch/main.nf index 518031ce7e8..f32df1ecba1 100644 --- a/tests/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/tests/modules/nf-core/hmmer/hmmsearch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMMER_HMMSEARCH } from '../../../../modules/nf-core/hmmer/hmmsearch/main.nf' +include { HMMER_HMMSEARCH } from '../../../../../modules/nf-core/hmmer/hmmsearch/main.nf' workflow test_hmmer_hmmsearch { diff --git a/tests/modules/nf-core/hmtnote/main.nf b/tests/modules/nf-core/hmtnote/main.nf index d914e6d02db..efaee619f38 100644 --- a/tests/modules/nf-core/hmtnote/main.nf +++ b/tests/modules/nf-core/hmtnote/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HMTNOTE } from '../../../modules/nf-core/hmtnote/main.nf' +include { HMTNOTE } from '../../../../modules/nf-core/hmtnote/main.nf' workflow test_hmtnote { diff --git a/tests/modules/nf-core/homer/annotatepeaks/main.nf b/tests/modules/nf-core/homer/annotatepeaks/main.nf index 5f0bdbdb744..cfd52c1ba49 100644 --- a/tests/modules/nf-core/homer/annotatepeaks/main.nf +++ b/tests/modules/nf-core/homer/annotatepeaks/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HOMER_ANNOTATEPEAKS } from '../../../../modules/nf-core/homer/annotatepeaks/main.nf' +include { HOMER_ANNOTATEPEAKS } from '../../../../../modules/nf-core/homer/annotatepeaks/main.nf' workflow test_homer_annotatepeaks { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/homer/findpeaks/main.nf b/tests/modules/nf-core/homer/findpeaks/main.nf index b1db0814cbd..2e9002bd6c7 100644 --- a/tests/modules/nf-core/homer/findpeaks/main.nf +++ b/tests/modules/nf-core/homer/findpeaks/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' -include { HOMER_FINDPEAKS } from '../../../../modules/nf-core/homer/findpeaks/main.nf' +include { HOMER_MAKETAGDIRECTORY } from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf' +include { HOMER_FINDPEAKS } from '../../../../../modules/nf-core/homer/findpeaks/main.nf' workflow test_homer_findpeaks { input = [[id:'test'], diff --git a/tests/modules/nf-core/homer/maketagdirectory/main.nf b/tests/modules/nf-core/homer/maketagdirectory/main.nf index cf0950c2bf8..1359fa5430c 100644 --- a/tests/modules/nf-core/homer/maketagdirectory/main.nf +++ b/tests/modules/nf-core/homer/maketagdirectory/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BED HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BAM -} from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' +} from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf' workflow test_homer_maketagdirectory_bed { input = [[id:'test'], diff --git a/tests/modules/nf-core/homer/makeucscfile/main.nf b/tests/modules/nf-core/homer/makeucscfile/main.nf index 243687696b1..f4649462e8a 100644 --- a/tests/modules/nf-core/homer/makeucscfile/main.nf +++ b/tests/modules/nf-core/homer/makeucscfile/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' -include { HOMER_MAKEUCSCFILE } from '../../../../modules/nf-core/homer/makeucscfile/main.nf' +include { HOMER_MAKETAGDIRECTORY } from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf' +include { HOMER_MAKEUCSCFILE } from '../../../../../modules/nf-core/homer/makeucscfile/main.nf' workflow test_homer_makeucscfile { input = [[id:'test'], diff --git a/tests/modules/nf-core/homer/pos2bed/main.nf b/tests/modules/nf-core/homer/pos2bed/main.nf index 3d814f60728..4eb9269541d 100644 --- a/tests/modules/nf-core/homer/pos2bed/main.nf +++ b/tests/modules/nf-core/homer/pos2bed/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/nf-core/homer/maketagdirectory/main.nf' -include { HOMER_FINDPEAKS } from '../../../../modules/nf-core/homer/findpeaks/main.nf' -include { HOMER_POS2BED } from '../../../../modules/nf-core/homer/pos2bed/main.nf' +include { HOMER_MAKETAGDIRECTORY } from '../../../../../modules/nf-core/homer/maketagdirectory/main.nf' +include { HOMER_FINDPEAKS } from '../../../../../modules/nf-core/homer/findpeaks/main.nf' +include { HOMER_POS2BED } from '../../../../../modules/nf-core/homer/pos2bed/main.nf' workflow test_homer_pos2bed { input = [[id:'test'], diff --git a/tests/modules/nf-core/hpsuissero/main.nf b/tests/modules/nf-core/hpsuissero/main.nf index 03cde9e7bfe..4bda9843fe9 100644 --- a/tests/modules/nf-core/hpsuissero/main.nf +++ b/tests/modules/nf-core/hpsuissero/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { HPSUISSERO } from '../../../modules/nf-core/hpsuissero/main.nf' +include { HPSUISSERO } from '../../../../modules/nf-core/hpsuissero/main.nf' workflow test_hpsuissero { diff --git a/tests/modules/nf-core/ichorcna/createpon/main.nf b/tests/modules/nf-core/ichorcna/createpon/main.nf index b5fadf62ecb..9d9a291abb3 100644 --- a/tests/modules/nf-core/ichorcna/createpon/main.nf +++ b/tests/modules/nf-core/ichorcna/createpon/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ICHORCNA_CREATEPON } from '../../../../modules/nf-core/ichorcna/createpon/main.nf' +include { ICHORCNA_CREATEPON } from '../../../../../modules/nf-core/ichorcna/createpon/main.nf' workflow test_ichorcna_createpon { diff --git a/tests/modules/nf-core/ichorcna/run/main.nf b/tests/modules/nf-core/ichorcna/run/main.nf index fc87f133b9d..ed57cccc46c 100644 --- a/tests/modules/nf-core/ichorcna/run/main.nf +++ b/tests/modules/nf-core/ichorcna/run/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { ICHORCNA_RUN } from '../../../../modules/nf-core/ichorcna/run/main.nf' -include { HMMCOPY_READCOUNTER } from '../../../../modules/nf-core/hmmcopy/readcounter/main.nf' -include { HMMCOPY_GCCOUNTER } from '../../../../modules/nf-core/hmmcopy/gccounter/main.nf' -include { HMMCOPY_MAPCOUNTER } from '../../../../modules/nf-core/hmmcopy/mapcounter/main.nf' -include { HMMCOPY_GENERATEMAP } from '../../../../modules/nf-core/hmmcopy/generatemap/main.nf' +include { ICHORCNA_RUN } from '../../../../../modules/nf-core/ichorcna/run/main.nf' +include { HMMCOPY_READCOUNTER } from '../../../../../modules/nf-core/hmmcopy/readcounter/main.nf' +include { HMMCOPY_GCCOUNTER } from '../../../../../modules/nf-core/hmmcopy/gccounter/main.nf' +include { HMMCOPY_MAPCOUNTER } from '../../../../../modules/nf-core/hmmcopy/mapcounter/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../../modules/nf-core/hmmcopy/generatemap/main.nf' workflow test_ichorcna_run_no_panel { diff --git a/tests/modules/nf-core/idr/main.nf b/tests/modules/nf-core/idr/main.nf index 67998a1a641..f532e8f5994 100644 --- a/tests/modules/nf-core/idr/main.nf +++ b/tests/modules/nf-core/idr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IDR } from '../../../modules/nf-core/idr/main.nf' +include { IDR } from '../../../../modules/nf-core/idr/main.nf' workflow test_idr_narrowpeak { diff --git a/tests/modules/nf-core/imputeme/vcftoprs/main.nf b/tests/modules/nf-core/imputeme/vcftoprs/main.nf index a42061bbe6a..fad879a2bb3 100644 --- a/tests/modules/nf-core/imputeme/vcftoprs/main.nf +++ b/tests/modules/nf-core/imputeme/vcftoprs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IMPUTEME_VCFTOPRS } from '../../../../modules/nf-core/imputeme/vcftoprs/main.nf' +include { IMPUTEME_VCFTOPRS } from '../../../../../modules/nf-core/imputeme/vcftoprs/main.nf' workflow test_imputeme_vcftoprs { diff --git a/tests/modules/nf-core/instrain/profile/main.nf b/tests/modules/nf-core/instrain/profile/main.nf index f5f4aba4350..83239d6085d 100644 --- a/tests/modules/nf-core/instrain/profile/main.nf +++ b/tests/modules/nf-core/instrain/profile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { INSTRAIN_PROFILE } from '../../../../modules/nf-core/instrain/profile/main.nf' +include { INSTRAIN_PROFILE } from '../../../../../modules/nf-core/instrain/profile/main.nf' workflow test_instrain_profile { diff --git a/tests/modules/nf-core/iqtree/main.nf b/tests/modules/nf-core/iqtree/main.nf index 071965b8cb1..abf2e8cbb93 100644 --- a/tests/modules/nf-core/iqtree/main.nf +++ b/tests/modules/nf-core/iqtree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IQTREE } from '../../../modules/nf-core/iqtree/main.nf' +include { IQTREE } from '../../../../modules/nf-core/iqtree/main.nf' workflow test_iqtree { diff --git a/tests/modules/nf-core/ismapper/main.nf b/tests/modules/nf-core/ismapper/main.nf index 5f816e18c80..01e0b384829 100644 --- a/tests/modules/nf-core/ismapper/main.nf +++ b/tests/modules/nf-core/ismapper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ISMAPPER } from '../../../modules/nf-core/ismapper/main.nf' +include { ISMAPPER } from '../../../../modules/nf-core/ismapper/main.nf' workflow test_ismapper { diff --git a/tests/modules/nf-core/isoseq3/cluster/main.nf b/tests/modules/nf-core/isoseq3/cluster/main.nf index 82cce6665e5..3f586d9a5f5 100644 --- a/tests/modules/nf-core/isoseq3/cluster/main.nf +++ b/tests/modules/nf-core/isoseq3/cluster/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ISOSEQ3_CLUSTER } from '../../../../modules/nf-core/isoseq3/cluster/main.nf' +include { ISOSEQ3_CLUSTER } from '../../../../../modules/nf-core/isoseq3/cluster/main.nf' workflow test_isoseq3_cluster { diff --git a/tests/modules/nf-core/isoseq3/refine/main.nf b/tests/modules/nf-core/isoseq3/refine/main.nf index da96361e67f..1ebafad4af2 100644 --- a/tests/modules/nf-core/isoseq3/refine/main.nf +++ b/tests/modules/nf-core/isoseq3/refine/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ISOSEQ3_REFINE } from '../../../../modules/nf-core/isoseq3/refine/main' +include { ISOSEQ3_REFINE } from '../../../../../modules/nf-core/isoseq3/refine/main' workflow test_isoseq3_refine { diff --git a/tests/modules/nf-core/ivar/consensus/main.nf b/tests/modules/nf-core/ivar/consensus/main.nf index ec75d8c3f36..37ce0f8f17e 100644 --- a/tests/modules/nf-core/ivar/consensus/main.nf +++ b/tests/modules/nf-core/ivar/consensus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IVAR_CONSENSUS } from '../../../../modules/nf-core/ivar/consensus/main.nf' +include { IVAR_CONSENSUS } from '../../../../../modules/nf-core/ivar/consensus/main.nf' workflow test_ivar_consensus { diff --git a/tests/modules/nf-core/ivar/trim/main.nf b/tests/modules/nf-core/ivar/trim/main.nf index 915cf904ee7..550ce62c25e 100644 --- a/tests/modules/nf-core/ivar/trim/main.nf +++ b/tests/modules/nf-core/ivar/trim/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IVAR_TRIM } from '../../../../modules/nf-core/ivar/trim/main.nf' +include { IVAR_TRIM } from '../../../../../modules/nf-core/ivar/trim/main.nf' workflow test_ivar_trim { input = [ [ id:'test'], diff --git a/tests/modules/nf-core/ivar/variants/main.nf b/tests/modules/nf-core/ivar/variants/main.nf index bd3c4f05019..b8dd56b5ba3 100644 --- a/tests/modules/nf-core/ivar/variants/main.nf +++ b/tests/modules/nf-core/ivar/variants/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { IVAR_VARIANTS } from '../../../../modules/nf-core/ivar/variants/main.nf' +include { IVAR_VARIANTS } from '../../../../../modules/nf-core/ivar/variants/main.nf' workflow test_ivar_variants_no_gff_no_mpileup { diff --git a/tests/modules/nf-core/jupyternotebook/main.nf b/tests/modules/nf-core/jupyternotebook/main.nf index c5fe8a3988c..80c3a568321 100644 --- a/tests/modules/nf-core/jupyternotebook/main.nf +++ b/tests/modules/nf-core/jupyternotebook/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { JUPYTERNOTEBOOK } from '../../../modules/nf-core/jupyternotebook/main.nf' -include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/nf-core/jupyternotebook/main.nf' -include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/nf-core/jupyternotebook/main.nf' +include { JUPYTERNOTEBOOK } from '../../../../modules/nf-core/jupyternotebook/main.nf' +include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../../modules/nf-core/jupyternotebook/main.nf' +include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../../modules/nf-core/jupyternotebook/main.nf' workflow test_jupyternotebook { diff --git a/tests/modules/nf-core/kaiju/kaiju/main.nf b/tests/modules/nf-core/kaiju/kaiju/main.nf index 48b8e7e13fc..c2b1d60e712 100644 --- a/tests/modules/nf-core/kaiju/kaiju/main.nf +++ b/tests/modules/nf-core/kaiju/kaiju/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { KAIJU_KAIJU } from '../../../../modules/nf-core/kaiju/kaiju/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf' workflow test_kaiju_kaiju_single_end { diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf index a56e8d193a6..62adf390caf 100644 --- a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf +++ b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { KAIJU_KAIJU } from '../../../../modules/nf-core/kaiju/kaiju/main.nf' -include { KAIJU_KAIJU2KRONA } from '../../../../modules/nf-core/kaiju/kaiju2krona/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf' +include { KAIJU_KAIJU2KRONA } from '../../../../../modules/nf-core/kaiju/kaiju2krona/main.nf' workflow test_kaiju_kaiju2krona { diff --git a/tests/modules/nf-core/kaiju/kaiju2table/main.nf b/tests/modules/nf-core/kaiju/kaiju2table/main.nf index b8d51be81ac..413a7b39a93 100644 --- a/tests/modules/nf-core/kaiju/kaiju2table/main.nf +++ b/tests/modules/nf-core/kaiju/kaiju2table/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { KAIJU_KAIJU } from '../../../../modules/nf-core/kaiju/kaiju/main.nf' -include { KAIJU_KAIJU2TABLE } from '../../../../modules/nf-core/kaiju/kaiju2table/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf' +include { KAIJU_KAIJU2TABLE } from '../../../../../modules/nf-core/kaiju/kaiju2table/main.nf' workflow test_kaiju_kaiju_single_end { diff --git a/tests/modules/nf-core/kallisto/index/main.nf b/tests/modules/nf-core/kallisto/index/main.nf index 83f51efcfed..3fe04ca9ecb 100644 --- a/tests/modules/nf-core/kallisto/index/main.nf +++ b/tests/modules/nf-core/kallisto/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KALLISTO_INDEX } from '../../../../modules/nf-core/kallisto/index/main.nf' +include { KALLISTO_INDEX } from '../../../../../modules/nf-core/kallisto/index/main.nf' workflow test_kallisto_index { diff --git a/tests/modules/nf-core/kallistobustools/count/main.nf b/tests/modules/nf-core/kallistobustools/count/main.nf index 9f193b564c9..ff7671ec5af 100644 --- a/tests/modules/nf-core/kallistobustools/count/main.nf +++ b/tests/modules/nf-core/kallistobustools/count/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { KALLISTOBUSTOOLS_REF } from '../../../../modules/nf-core/kallistobustools/ref/main.nf' -include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/nf-core/kallistobustools/count/main.nf' +include { KALLISTOBUSTOOLS_REF } from '../../../../../modules/nf-core/kallistobustools/ref/main.nf' +include { KALLISTOBUSTOOLS_COUNT } from '../../../../../modules/nf-core/kallistobustools/count/main.nf' workflow test_kallistobustools_count { diff --git a/tests/modules/nf-core/kallistobustools/ref/main.nf b/tests/modules/nf-core/kallistobustools/ref/main.nf index 0d6d1c69c19..72bcd2d632a 100644 --- a/tests/modules/nf-core/kallistobustools/ref/main.nf +++ b/tests/modules/nf-core/kallistobustools/ref/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KALLISTOBUSTOOLS_REF } from '../../../../modules/nf-core/kallistobustools/ref/main.nf' +include { KALLISTOBUSTOOLS_REF } from '../../../../../modules/nf-core/kallistobustools/ref/main.nf' workflow test_kallistobustools_ref_standard { diff --git a/tests/modules/nf-core/kat/hist/main.nf b/tests/modules/nf-core/kat/hist/main.nf index 9c1356700b6..093674accdf 100644 --- a/tests/modules/nf-core/kat/hist/main.nf +++ b/tests/modules/nf-core/kat/hist/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KAT_HIST } from '../../../../modules/nf-core/kat/hist/main.nf' +include { KAT_HIST } from '../../../../../modules/nf-core/kat/hist/main.nf' workflow test_kat_hist_single_end { diff --git a/tests/modules/nf-core/khmer/normalizebymedian/main.nf b/tests/modules/nf-core/khmer/normalizebymedian/main.nf index c26fb09f0ba..26727165f04 100644 --- a/tests/modules/nf-core/khmer/normalizebymedian/main.nf +++ b/tests/modules/nf-core/khmer/normalizebymedian/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { SEQTK_MERGEPE } from '../../../../modules/nf-core/seqtk/mergepe/main.nf' -include { KHMER_NORMALIZEBYMEDIAN } from '../../../../modules/nf-core/khmer/normalizebymedian/main.nf' -include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../modules/nf-core/khmer/normalizebymedian/main.nf' +include { SEQTK_MERGEPE } from '../../../../../modules/nf-core/seqtk/mergepe/main.nf' +include { KHMER_NORMALIZEBYMEDIAN } from '../../../../../modules/nf-core/khmer/normalizebymedian/main.nf' +include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../../modules/nf-core/khmer/normalizebymedian/main.nf' workflow test_khmer_normalizebymedian_only_pe { diff --git a/tests/modules/nf-core/khmer/uniquekmers/main.nf b/tests/modules/nf-core/khmer/uniquekmers/main.nf index afcbe13bc60..4dae054890e 100644 --- a/tests/modules/nf-core/khmer/uniquekmers/main.nf +++ b/tests/modules/nf-core/khmer/uniquekmers/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KHMER_UNIQUEKMERS } from '../../../../modules/nf-core/khmer/uniquekmers/main.nf' +include { KHMER_UNIQUEKMERS } from '../../../../../modules/nf-core/khmer/uniquekmers/main.nf' workflow test_khmer_uniquekmers { diff --git a/tests/modules/nf-core/kleborate/main.nf b/tests/modules/nf-core/kleborate/main.nf index c50153bdfc4..93c765c74f9 100644 --- a/tests/modules/nf-core/kleborate/main.nf +++ b/tests/modules/nf-core/kleborate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KLEBORATE } from '../../../modules/nf-core/kleborate/main.nf' +include { KLEBORATE } from '../../../../modules/nf-core/kleborate/main.nf' workflow test_kleborate { diff --git a/tests/modules/nf-core/kraken2/kraken2/main.nf b/tests/modules/nf-core/kraken2/kraken2/main.nf index 4570817668c..ac27253c8ee 100644 --- a/tests/modules/nf-core/kraken2/kraken2/main.nf +++ b/tests/modules/nf-core/kraken2/kraken2/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main.nf' workflow test_kraken2_kraken2_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/krakentools/combinekreports/main.nf b/tests/modules/nf-core/krakentools/combinekreports/main.nf index 6cb92667848..27f453f4cab 100644 --- a/tests/modules/nf-core/krakentools/combinekreports/main.nf +++ b/tests/modules/nf-core/krakentools/combinekreports/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main' -include { KRAKENTOOLS_COMBINEKREPORTS } from '../../../../modules/nf-core/krakentools/combinekreports/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main' +include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main' +include { KRAKENTOOLS_COMBINEKREPORTS } from '../../../../../modules/nf-core/krakentools/combinekreports/main.nf' workflow test_krakentools_combinekreports { diff --git a/tests/modules/nf-core/krakentools/kreport2krona/main.nf b/tests/modules/nf-core/krakentools/kreport2krona/main.nf index 28f79ea08a2..5951acc070d 100644 --- a/tests/modules/nf-core/krakentools/kreport2krona/main.nf +++ b/tests/modules/nf-core/krakentools/kreport2krona/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main' -include { KRAKEN2_KRAKEN2 } from '../../../../modules/nf-core/kraken2/kraken2/main' -include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../modules/nf-core/krakentools/kreport2krona/main' +include { UNTAR } from '../../../../../modules/nf-core/untar/main' +include { KRAKEN2_KRAKEN2 } from '../../../../../modules/nf-core/kraken2/kraken2/main' +include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../../modules/nf-core/krakentools/kreport2krona/main' workflow test_krakentools_kreport2krona { diff --git a/tests/modules/nf-core/krona/kronadb/main.nf b/tests/modules/nf-core/krona/kronadb/main.nf index 2a701b5cb6f..b35b06a430b 100644 --- a/tests/modules/nf-core/krona/kronadb/main.nf +++ b/tests/modules/nf-core/krona/kronadb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KRONA_KRONADB } from '../../../../modules/nf-core/krona/kronadb/main.nf' +include { KRONA_KRONADB } from '../../../../../modules/nf-core/krona/kronadb/main.nf' workflow test_krona_kronadb { KRONA_KRONADB ( ) diff --git a/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf index e9029b6f802..a267df50b2a 100644 --- a/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf +++ b/tests/modules/nf-core/krona/ktimporttaxonomy/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS } from '../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf' -include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf' +include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS } from '../../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf' +include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../../modules/nf-core/krona/ktimporttaxonomy/main.nf' workflow test_krona_ktimporttaxonomy_reads { diff --git a/tests/modules/nf-core/krona/ktimporttext/main.nf b/tests/modules/nf-core/krona/ktimporttext/main.nf index fef8403811c..ee51b769fea 100644 --- a/tests/modules/nf-core/krona/ktimporttext/main.nf +++ b/tests/modules/nf-core/krona/ktimporttext/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KRONA_KTIMPORTTEXT } from '../../../../modules/nf-core/krona/ktimporttext/main.nf' +include { KRONA_KTIMPORTTEXT } from '../../../../../modules/nf-core/krona/ktimporttext/main.nf' workflow test_krona_ktimporttext_multi { diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf index b1165675f3f..2323ba7d811 100644 --- a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/nf-core/krona/ktupdatetaxonomy/main.nf' +include { KRONA_KTUPDATETAXONOMY } from '../../../../../modules/nf-core/krona/ktupdatetaxonomy/main.nf' workflow test_krona_ktupdatetaxonomy { KRONA_KTUPDATETAXONOMY ( ) diff --git a/tests/modules/nf-core/last/dotplot/main.nf b/tests/modules/nf-core/last/dotplot/main.nf index ced2e579994..1004535c6f6 100644 --- a/tests/modules/nf-core/last/dotplot/main.nf +++ b/tests/modules/nf-core/last/dotplot/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_DOTPLOT } from '../../../../modules/nf-core/last/dotplot/main.nf' +include { LAST_DOTPLOT } from '../../../../../modules/nf-core/last/dotplot/main.nf' workflow test_last_dotplot { diff --git a/tests/modules/nf-core/last/lastal/main.nf b/tests/modules/nf-core/last/lastal/main.nf index b47518f3b5c..64162a944b3 100644 --- a/tests/modules/nf-core/last/lastal/main.nf +++ b/tests/modules/nf-core/last/lastal/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { LAST_LASTAL } from '../../../../modules/nf-core/last/lastal/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { LAST_LASTAL } from '../../../../../modules/nf-core/last/lastal/main.nf' workflow test_last_lastal_with_dummy_param_file { diff --git a/tests/modules/nf-core/last/lastdb/main.nf b/tests/modules/nf-core/last/lastdb/main.nf index db1c166f3a7..56087905045 100644 --- a/tests/modules/nf-core/last/lastdb/main.nf +++ b/tests/modules/nf-core/last/lastdb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_LASTDB } from '../../../../modules/nf-core/last/lastdb/main.nf' +include { LAST_LASTDB } from '../../../../../modules/nf-core/last/lastdb/main.nf' workflow test_last_lastdb { diff --git a/tests/modules/nf-core/last/mafconvert/main.nf b/tests/modules/nf-core/last/mafconvert/main.nf index f99b4c468f5..d04591be1b1 100644 --- a/tests/modules/nf-core/last/mafconvert/main.nf +++ b/tests/modules/nf-core/last/mafconvert/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_MAFCONVERT } from '../../../../modules/nf-core/last/mafconvert/main.nf' +include { LAST_MAFCONVERT } from '../../../../../modules/nf-core/last/mafconvert/main.nf' workflow test_last_mafconvert { diff --git a/tests/modules/nf-core/last/mafswap/main.nf b/tests/modules/nf-core/last/mafswap/main.nf index 267ae0664e0..49eef17c378 100644 --- a/tests/modules/nf-core/last/mafswap/main.nf +++ b/tests/modules/nf-core/last/mafswap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_MAFSWAP } from '../../../../modules/nf-core/last/mafswap/main.nf' +include { LAST_MAFSWAP } from '../../../../../modules/nf-core/last/mafswap/main.nf' workflow test_last_mafswap { diff --git a/tests/modules/nf-core/last/postmask/main.nf b/tests/modules/nf-core/last/postmask/main.nf index 7de628ce610..697a431e8a8 100644 --- a/tests/modules/nf-core/last/postmask/main.nf +++ b/tests/modules/nf-core/last/postmask/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_POSTMASK } from '../../../../modules/nf-core/last/postmask/main.nf' +include { LAST_POSTMASK } from '../../../../../modules/nf-core/last/postmask/main.nf' workflow test_last_postmask { diff --git a/tests/modules/nf-core/last/split/main.nf b/tests/modules/nf-core/last/split/main.nf index c48fda38aa4..df8f20cfc36 100644 --- a/tests/modules/nf-core/last/split/main.nf +++ b/tests/modules/nf-core/last/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LAST_SPLIT } from '../../../../modules/nf-core/last/split/main.nf' +include { LAST_SPLIT } from '../../../../../modules/nf-core/last/split/main.nf' workflow test_last_split { diff --git a/tests/modules/nf-core/last/train/main.nf b/tests/modules/nf-core/last/train/main.nf index dc1daa32fb7..a166fea8887 100644 --- a/tests/modules/nf-core/last/train/main.nf +++ b/tests/modules/nf-core/last/train/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { LAST_TRAIN } from '../../../../modules/nf-core/last/train/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { LAST_TRAIN } from '../../../../../modules/nf-core/last/train/main.nf' workflow test_last_train { diff --git a/tests/modules/nf-core/leehom/main.nf b/tests/modules/nf-core/leehom/main.nf index 8c0326a12a6..e91653319b5 100644 --- a/tests/modules/nf-core/leehom/main.nf +++ b/tests/modules/nf-core/leehom/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { LEEHOM } from '../../../modules/nf-core/leehom/main.nf' -include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main.nf' +include { LEEHOM } from '../../../../modules/nf-core/leehom/main.nf' +include { SAMTOOLS_VIEW } from '../../../../modules/nf-core/samtools/view/main.nf' workflow test_leehom_bam { diff --git a/tests/modules/nf-core/legsta/main.nf b/tests/modules/nf-core/legsta/main.nf index 6bf4588cd79..b74a9cf278a 100644 --- a/tests/modules/nf-core/legsta/main.nf +++ b/tests/modules/nf-core/legsta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LEGSTA } from '../../../modules/nf-core/legsta/main.nf' +include { LEGSTA } from '../../../../modules/nf-core/legsta/main.nf' workflow test_legsta { diff --git a/tests/modules/nf-core/lima/main.nf b/tests/modules/nf-core/lima/main.nf index 7b716fa5be3..921b8dcba78 100644 --- a/tests/modules/nf-core/lima/main.nf +++ b/tests/modules/nf-core/lima/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LIMA } from '../../../modules/nf-core/lima/main.nf' +include { LIMA } from '../../../../modules/nf-core/lima/main.nf' workflow test_lima_bam { diff --git a/tests/modules/nf-core/lissero/main.nf b/tests/modules/nf-core/lissero/main.nf index 712f6161e01..3387251d6f7 100644 --- a/tests/modules/nf-core/lissero/main.nf +++ b/tests/modules/nf-core/lissero/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LISSERO } from '../../../modules/nf-core/lissero/main.nf' +include { LISSERO } from '../../../../modules/nf-core/lissero/main.nf' workflow test_lissero { diff --git a/tests/modules/nf-core/lofreq/call/main.nf b/tests/modules/nf-core/lofreq/call/main.nf index d00e98a7592..0492da377e5 100644 --- a/tests/modules/nf-core/lofreq/call/main.nf +++ b/tests/modules/nf-core/lofreq/call/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_CALL } from '../../../../modules/nf-core/lofreq/call/main.nf' +include { LOFREQ_CALL } from '../../../../../modules/nf-core/lofreq/call/main.nf' workflow test_lofreq_call { diff --git a/tests/modules/nf-core/lofreq/callparallel/main.nf b/tests/modules/nf-core/lofreq/callparallel/main.nf index cae4505e8cb..dacc323854b 100644 --- a/tests/modules/nf-core/lofreq/callparallel/main.nf +++ b/tests/modules/nf-core/lofreq/callparallel/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_CALLPARALLEL } from '../../../../modules/nf-core/lofreq/callparallel/main.nf' +include { LOFREQ_CALLPARALLEL } from '../../../../../modules/nf-core/lofreq/callparallel/main.nf' workflow test_lofreq_callparallel { diff --git a/tests/modules/nf-core/lofreq/filter/main.nf b/tests/modules/nf-core/lofreq/filter/main.nf index db2b5fd03c8..d775ffb4d2f 100644 --- a/tests/modules/nf-core/lofreq/filter/main.nf +++ b/tests/modules/nf-core/lofreq/filter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_FILTER } from '../../../../modules/nf-core/lofreq/filter/main.nf' +include { LOFREQ_FILTER } from '../../../../../modules/nf-core/lofreq/filter/main.nf' workflow test_lofreq_filter { diff --git a/tests/modules/nf-core/lofreq/indelqual/main.nf b/tests/modules/nf-core/lofreq/indelqual/main.nf index c8b69b94c7d..8fe400bb857 100644 --- a/tests/modules/nf-core/lofreq/indelqual/main.nf +++ b/tests/modules/nf-core/lofreq/indelqual/main.nf @@ -3,7 +3,7 @@ nextflow.enable.dsl = 2 -include { LOFREQ_INDELQUAL } from '../../../../modules/nf-core/lofreq/indelqual/main.nf' +include { LOFREQ_INDELQUAL } from '../../../../../modules/nf-core/lofreq/indelqual/main.nf' workflow test_lofreq_indelqual { diff --git a/tests/modules/nf-core/macrel/contigs/main.nf b/tests/modules/nf-core/macrel/contigs/main.nf index 986a1a20e34..1798753831e 100644 --- a/tests/modules/nf-core/macrel/contigs/main.nf +++ b/tests/modules/nf-core/macrel/contigs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MACREL_CONTIGS } from '../../../../modules/nf-core/macrel/contigs/main.nf' +include { MACREL_CONTIGS } from '../../../../../modules/nf-core/macrel/contigs/main.nf' workflow test_macrel_contigs { diff --git a/tests/modules/nf-core/macs2/callpeak/main.nf b/tests/modules/nf-core/macs2/callpeak/main.nf index a65675b5c80..0e41229f8a0 100644 --- a/tests/modules/nf-core/macs2/callpeak/main.nf +++ b/tests/modules/nf-core/macs2/callpeak/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { MACS2_CALLPEAK } from '../../../../modules/nf-core/macs2/callpeak/main.nf' -include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/nf-core/macs2/callpeak/main.nf' -include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/nf-core/macs2/callpeak/main.nf' +include { MACS2_CALLPEAK } from '../../../../../modules/nf-core/macs2/callpeak/main.nf' +include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../../modules/nf-core/macs2/callpeak/main.nf' +include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../../modules/nf-core/macs2/callpeak/main.nf' workflow test_macs2_callpeak_bed { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/mafft/main.nf b/tests/modules/nf-core/mafft/main.nf index ee91863f6c1..c3e7f0782ab 100644 --- a/tests/modules/nf-core/mafft/main.nf +++ b/tests/modules/nf-core/mafft/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAFFT } from '../../../modules/nf-core/mafft/main.nf' +include { MAFFT } from '../../../../modules/nf-core/mafft/main.nf' workflow test_mafft { diff --git a/tests/modules/nf-core/malt/build_test/main.nf b/tests/modules/nf-core/malt/build_test/main.nf index 95d01942edc..dbf7fd3ebe6 100644 --- a/tests/modules/nf-core/malt/build_test/main.nf +++ b/tests/modules/nf-core/malt/build_test/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf' -include { MALT_BUILD } from '../../../../modules/nf-core/malt/build/main.nf' +include { UNZIP } from '../../../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../../../modules/nf-core/malt/build/main.nf' workflow test_malt_build { fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/malt/run/main.nf b/tests/modules/nf-core/malt/run/main.nf index 85cee2c879d..fb40f05b26e 100644 --- a/tests/modules/nf-core/malt/run/main.nf +++ b/tests/modules/nf-core/malt/run/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf' -include { MALT_BUILD } from '../../../../modules/nf-core/malt/build/main.nf' -include { MALT_RUN } from '../../../../modules/nf-core/malt/run/main.nf' +include { UNZIP } from '../../../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../../../modules/nf-core/malt/build/main.nf' +include { MALT_RUN } from '../../../../../modules/nf-core/malt/run/main.nf' workflow test_malt_run { diff --git a/tests/modules/nf-core/maltextract/main.nf b/tests/modules/nf-core/maltextract/main.nf index 88b889e4481..5ecbbab9515 100644 --- a/tests/modules/nf-core/maltextract/main.nf +++ b/tests/modules/nf-core/maltextract/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { UNZIP as UNZIP_MALT } from '../../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/nf-core/unzip/main.nf' -include { MALT_BUILD } from '../../../modules/nf-core/malt/build/main.nf' -include { MALT_RUN } from '../../../modules/nf-core/malt/run/main.nf' -include { MALTEXTRACT } from '../../../modules/nf-core/maltextract/main.nf' +include { UNZIP as UNZIP_MALT } from '../../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_MALTEXTRACT } from '../../../../modules/nf-core/unzip/main.nf' +include { MALT_BUILD } from '../../../../modules/nf-core/malt/build/main.nf' +include { MALT_RUN } from '../../../../modules/nf-core/malt/run/main.nf' +include { MALTEXTRACT } from '../../../../modules/nf-core/maltextract/main.nf' workflow test_maltextract { diff --git a/tests/modules/nf-core/manta/convertinversion/main.nf b/tests/modules/nf-core/manta/convertinversion/main.nf index 0ad19c74686..b51b7057918 100644 --- a/tests/modules/nf-core/manta/convertinversion/main.nf +++ b/tests/modules/nf-core/manta/convertinversion/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MANTA_CONVERTINVERSION } from '../../../../modules/nf-core/manta/convertinversion/main.nf' -include { MANTA_TUMORONLY } from '../../../../modules/nf-core/manta/tumoronly/main.nf' +include { MANTA_CONVERTINVERSION } from '../../../../../modules/nf-core/manta/convertinversion/main.nf' +include { MANTA_TUMORONLY } from '../../../../../modules/nf-core/manta/tumoronly/main.nf' workflow test_manta_convertinversion { diff --git a/tests/modules/nf-core/manta/germline/main.nf b/tests/modules/nf-core/manta/germline/main.nf index 5bc0476d558..e949d73470d 100644 --- a/tests/modules/nf-core/manta/germline/main.nf +++ b/tests/modules/nf-core/manta/germline/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MANTA_GERMLINE } from '../../../../modules/nf-core/manta/germline/main.nf' +include { MANTA_GERMLINE } from '../../../../../modules/nf-core/manta/germline/main.nf' workflow test_manta_germline { input = [ diff --git a/tests/modules/nf-core/manta/somatic/main.nf b/tests/modules/nf-core/manta/somatic/main.nf index 71bca3101af..2fdceb00011 100644 --- a/tests/modules/nf-core/manta/somatic/main.nf +++ b/tests/modules/nf-core/manta/somatic/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MANTA_SOMATIC } from '../../../../modules/nf-core/manta/somatic/main.nf' +include { MANTA_SOMATIC } from '../../../../../modules/nf-core/manta/somatic/main.nf' workflow test_manta_somatic { diff --git a/tests/modules/nf-core/manta/tumoronly/main.nf b/tests/modules/nf-core/manta/tumoronly/main.nf index e120048c2f2..dccf5591ba2 100644 --- a/tests/modules/nf-core/manta/tumoronly/main.nf +++ b/tests/modules/nf-core/manta/tumoronly/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MANTA_TUMORONLY } from '../../../../modules/nf-core/manta/tumoronly/main.nf' +include { MANTA_TUMORONLY } from '../../../../../modules/nf-core/manta/tumoronly/main.nf' workflow test_manta_tumoronly { input = [ diff --git a/tests/modules/nf-core/mapdamage2/main.nf b/tests/modules/nf-core/mapdamage2/main.nf index 105f24dec80..47e550c6e96 100644 --- a/tests/modules/nf-core/mapdamage2/main.nf +++ b/tests/modules/nf-core/mapdamage2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAPDAMAGE2 } from '../../../modules/nf-core/mapdamage2/main.nf' +include { MAPDAMAGE2 } from '../../../../modules/nf-core/mapdamage2/main.nf' workflow test_mapdamage2 { diff --git a/tests/modules/nf-core/mash/dist/main.nf b/tests/modules/nf-core/mash/dist/main.nf index 75a01e0ace0..30b37a746c7 100644 --- a/tests/modules/nf-core/mash/dist/main.nf +++ b/tests/modules/nf-core/mash/dist/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MASH_DIST } from '../../../../modules/nf-core/mash/dist/main.nf' +include { MASH_DIST } from '../../../../../modules/nf-core/mash/dist/main.nf' workflow test_mash_dist { diff --git a/tests/modules/nf-core/mash/screen/main.nf b/tests/modules/nf-core/mash/screen/main.nf index 40345d57017..91675faa581 100644 --- a/tests/modules/nf-core/mash/screen/main.nf +++ b/tests/modules/nf-core/mash/screen/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MASH_SKETCH } from '../../../../modules/nf-core/mash/sketch/main.nf' -include { MASH_SCREEN } from '../../../../modules/nf-core/mash/screen/main.nf' +include { MASH_SKETCH } from '../../../../../modules/nf-core/mash/sketch/main.nf' +include { MASH_SCREEN } from '../../../../../modules/nf-core/mash/screen/main.nf' workflow test_mash_screen { diff --git a/tests/modules/nf-core/mash/sketch/main.nf b/tests/modules/nf-core/mash/sketch/main.nf index 5a95895876c..6fe6e93f0cd 100644 --- a/tests/modules/nf-core/mash/sketch/main.nf +++ b/tests/modules/nf-core/mash/sketch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MASH_SKETCH } from '../../../../modules/nf-core/mash/sketch/main.nf' +include { MASH_SKETCH } from '../../../../../modules/nf-core/mash/sketch/main.nf' workflow test_mash_sketch { diff --git a/tests/modules/nf-core/mashtree/main.nf b/tests/modules/nf-core/mashtree/main.nf index 63a03887c70..8ffbab037b1 100644 --- a/tests/modules/nf-core/mashtree/main.nf +++ b/tests/modules/nf-core/mashtree/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MASHTREE } from '../../../modules/nf-core/mashtree/main.nf' +include { MASHTREE } from '../../../../modules/nf-core/mashtree/main.nf' workflow test_mashtree { diff --git a/tests/modules/nf-core/maxbin2/main.nf b/tests/modules/nf-core/maxbin2/main.nf index d6d5d2c4988..2eb6cb45213 100644 --- a/tests/modules/nf-core/maxbin2/main.nf +++ b/tests/modules/nf-core/maxbin2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAXBIN2 } from '../../../modules/nf-core/maxbin2/main.nf' +include { MAXBIN2 } from '../../../../modules/nf-core/maxbin2/main.nf' workflow test_maxbin2 { diff --git a/tests/modules/nf-core/maxquant/lfq/main.nf b/tests/modules/nf-core/maxquant/lfq/main.nf index ee1c92ae33a..bee3c82599b 100644 --- a/tests/modules/nf-core/maxquant/lfq/main.nf +++ b/tests/modules/nf-core/maxquant/lfq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MAXQUANT_LFQ } from '../../../../modules/nf-core/maxquant/lfq/main.nf' addParams( options: [:] ) +include { MAXQUANT_LFQ } from '../../../../../modules/nf-core/maxquant/lfq/main.nf' addParams( options: [:] ) workflow test_maxquant_lfq { diff --git a/tests/modules/nf-core/mcroni/main.nf b/tests/modules/nf-core/mcroni/main.nf index bd11b702822..c1eeeb5fa30 100644 --- a/tests/modules/nf-core/mcroni/main.nf +++ b/tests/modules/nf-core/mcroni/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MCRONI } from '../../../modules/nf-core/mcroni/main.nf' +include { MCRONI } from '../../../../modules/nf-core/mcroni/main.nf' workflow test_mcroni { diff --git a/tests/modules/nf-core/md5sum/main.nf b/tests/modules/nf-core/md5sum/main.nf index 1995b2a921d..56b22acee1e 100644 --- a/tests/modules/nf-core/md5sum/main.nf +++ b/tests/modules/nf-core/md5sum/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MD5SUM } from '../../../modules/nf-core/md5sum/main.nf' +include { MD5SUM } from '../../../../modules/nf-core/md5sum/main.nf' workflow test_md5sum { diff --git a/tests/modules/nf-core/medaka/main.nf b/tests/modules/nf-core/medaka/main.nf index 4fe483d009f..3ae6f6e7fdb 100644 --- a/tests/modules/nf-core/medaka/main.nf +++ b/tests/modules/nf-core/medaka/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MEDAKA } from '../../../modules/nf-core/medaka/main.nf' +include { MEDAKA } from '../../../../modules/nf-core/medaka/main.nf' workflow test_medaka { diff --git a/tests/modules/nf-core/megahit/main.nf b/tests/modules/nf-core/megahit/main.nf index 78b0fc49cca..57369265e98 100644 --- a/tests/modules/nf-core/megahit/main.nf +++ b/tests/modules/nf-core/megahit/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MEGAHIT } from '../../../modules/nf-core/megahit/main.nf' +include { MEGAHIT } from '../../../../modules/nf-core/megahit/main.nf' workflow test_megahit { diff --git a/tests/modules/nf-core/megan/daa2info/main.nf b/tests/modules/nf-core/megan/daa2info/main.nf index 2ea860a8c37..52f0ee2ef26 100644 --- a/tests/modules/nf-core/megan/daa2info/main.nf +++ b/tests/modules/nf-core/megan/daa2info/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { DIAMOND_MAKEDB } from '../../../../modules/nf-core/diamond/makedb/main.nf' -include { DIAMOND_BLASTX } from '../../../../modules/nf-core/diamond/blastx/main.nf' -include { MEGAN_DAA2INFO } from '../../../../modules/nf-core/megan/daa2info/main.nf' +include { DIAMOND_MAKEDB } from '../../../../../modules/nf-core/diamond/makedb/main.nf' +include { DIAMOND_BLASTX } from '../../../../../modules/nf-core/diamond/blastx/main.nf' +include { MEGAN_DAA2INFO } from '../../../../../modules/nf-core/megan/daa2info/main.nf' workflow test_megan_daa2info { diff --git a/tests/modules/nf-core/megan/rma2info/main.nf b/tests/modules/nf-core/megan/rma2info/main.nf index 7b78ae5b089..c8c76787724 100644 --- a/tests/modules/nf-core/megan/rma2info/main.nf +++ b/tests/modules/nf-core/megan/rma2info/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MEGAN_RMA2INFO } from '../../../../modules/nf-core/megan/rma2info/main.nf' +include { MEGAN_RMA2INFO } from '../../../../../modules/nf-core/megan/rma2info/main.nf' workflow test_megan_rma2info { diff --git a/tests/modules/nf-core/meningotype/main.nf b/tests/modules/nf-core/meningotype/main.nf index eeee73c3247..14ff4d00728 100644 --- a/tests/modules/nf-core/meningotype/main.nf +++ b/tests/modules/nf-core/meningotype/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MENINGOTYPE } from '../../../modules/nf-core/meningotype/main.nf' +include { MENINGOTYPE } from '../../../../modules/nf-core/meningotype/main.nf' workflow test_meningotype { diff --git a/tests/modules/nf-core/merqury/main.nf b/tests/modules/nf-core/merqury/main.nf index c453ed28c75..7d525446512 100644 --- a/tests/modules/nf-core/merqury/main.nf +++ b/tests/modules/nf-core/merqury/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../modules/nf-core/meryl/count/main.nf' -include { MERYL_UNIONSUM } from '../../../modules/nf-core/meryl/unionsum/main.nf' -include { MERQURY } from '../../../modules/nf-core/merqury/main.nf' +include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_UNIONSUM } from '../../../../modules/nf-core/meryl/unionsum/main.nf' +include { MERQURY } from '../../../../modules/nf-core/merqury/main.nf' workflow test_merqury { diff --git a/tests/modules/nf-core/merquryfk/katcomp/main.nf b/tests/modules/nf-core/merquryfk/katcomp/main.nf index 32c2f68a70d..78857f85494 100644 --- a/tests/modules/nf-core/merquryfk/katcomp/main.nf +++ b/tests/modules/nf-core/merquryfk/katcomp/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK as FASTK1 } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { FASTK_FASTK as FASTK2 } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { MERQURYFK_KATCOMP } from '../../../../modules/nf-core/merquryfk/katcomp/main.nf' +include { FASTK_FASTK as FASTK1 } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { FASTK_FASTK as FASTK2 } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_KATCOMP } from '../../../../../modules/nf-core/merquryfk/katcomp/main.nf' workflow test_merquryfk_katcomp_png { diff --git a/tests/modules/nf-core/merquryfk/katgc/main.nf b/tests/modules/nf-core/merquryfk/katgc/main.nf index a398f991279..d16ef2a1673 100644 --- a/tests/modules/nf-core/merquryfk/katgc/main.nf +++ b/tests/modules/nf-core/merquryfk/katgc/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { MERQURYFK_KATGC } from '../../../../modules/nf-core/merquryfk/katgc/main.nf' +include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_KATGC } from '../../../../../modules/nf-core/merquryfk/katgc/main.nf' workflow test_merquryfk_katgc_png { diff --git a/tests/modules/nf-core/merquryfk/merquryfk/main.nf b/tests/modules/nf-core/merquryfk/merquryfk/main.nf index 4c08f12055c..282833a4240 100644 --- a/tests/modules/nf-core/merquryfk/merquryfk/main.nf +++ b/tests/modules/nf-core/merquryfk/merquryfk/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { MERQURYFK_MERQURYFK } from '../../../../modules/nf-core/merquryfk/merquryfk/main.nf' +include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_MERQURYFK } from '../../../../../modules/nf-core/merquryfk/merquryfk/main.nf' workflow test_merquryfk_merquryfk_png { diff --git a/tests/modules/nf-core/merquryfk/ploidyplot/main.nf b/tests/modules/nf-core/merquryfk/ploidyplot/main.nf index a9d52dd072c..26d228ed534 100644 --- a/tests/modules/nf-core/merquryfk/ploidyplot/main.nf +++ b/tests/modules/nf-core/merquryfk/ploidyplot/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { FASTK_FASTK } from '../../../../modules/nf-core/fastk/fastk/main.nf' -include { MERQURYFK_PLOIDYPLOT } from '../../../../modules/nf-core/merquryfk/ploidyplot/main.nf' +include { FASTK_FASTK } from '../../../../../modules/nf-core/fastk/fastk/main.nf' +include { MERQURYFK_PLOIDYPLOT } from '../../../../../modules/nf-core/merquryfk/ploidyplot/main.nf' workflow test_merquryfk_ploidyplot_png { diff --git a/tests/modules/nf-core/meryl/count/main.nf b/tests/modules/nf-core/meryl/count/main.nf index efd03eabd9c..cd71fb983da 100644 --- a/tests/modules/nf-core/meryl/count/main.nf +++ b/tests/modules/nf-core/meryl/count/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf' workflow test_meryl_count_single_end { diff --git a/tests/modules/nf-core/meryl/histogram/main.nf b/tests/modules/nf-core/meryl/histogram/main.nf index 57f6ebd7e6f..153a76d44bf 100644 --- a/tests/modules/nf-core/meryl/histogram/main.nf +++ b/tests/modules/nf-core/meryl/histogram/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' -include { MERYL_HISTOGRAM } from '../../../../modules/nf-core/meryl/histogram/main.nf' +include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_HISTOGRAM } from '../../../../../modules/nf-core/meryl/histogram/main.nf' workflow test_meryl_histogram { diff --git a/tests/modules/nf-core/meryl/unionsum/main.nf b/tests/modules/nf-core/meryl/unionsum/main.nf index cb3e13cb461..e4e767375ce 100644 --- a/tests/modules/nf-core/meryl/unionsum/main.nf +++ b/tests/modules/nf-core/meryl/unionsum/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MERYL_COUNT } from '../../../../modules/nf-core/meryl/count/main.nf' -include { MERYL_UNIONSUM } from '../../../../modules/nf-core/meryl/unionsum/main.nf' +include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf' +include { MERYL_UNIONSUM } from '../../../../../modules/nf-core/meryl/unionsum/main.nf' workflow test_meryl_unionsum_single_end { diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 1b67b1505f7..861e0cb5f74 100644 --- a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' workflow test_metabat2_jgisummarizebamcontigdepths { diff --git a/tests/modules/nf-core/metabat2/metabat2/main.nf b/tests/modules/nf-core/metabat2/metabat2/main.nf index 0122881926e..7bead547365 100644 --- a/tests/modules/nf-core/metabat2/metabat2/main.nf +++ b/tests/modules/nf-core/metabat2/metabat2/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { METABAT2_METABAT2 } from '../../../../modules/nf-core/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' +include { METABAT2_METABAT2 } from '../../../../../modules/nf-core/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' workflow test_metabat2_no_depth { diff --git a/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf index fa8695e0e92..eaa46a1acd5 100644 --- a/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf +++ b/tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { METAPHLAN3 } from '../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf' -include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../modules/nf-core/metaphlan3/mergemetaphlantables/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { METAPHLAN3 } from '../../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf' +include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../../modules/nf-core/metaphlan3/mergemetaphlantables/main.nf' workflow test_metaphlan3_mergemetaphlantables { diff --git a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf index cfba3b2dce4..4a0f7948f5c 100644 --- a/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf +++ b/tests/modules/nf-core/metaphlan3/metaphlan3/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { METAPHLAN3_METAPHLAN3 } from '../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { METAPHLAN3_METAPHLAN3 } from '../../../../../modules/nf-core/metaphlan3/metaphlan3/main.nf' workflow test_metaphlan3_single_end { diff --git a/tests/modules/nf-core/methyldackel/extract/main.nf b/tests/modules/nf-core/methyldackel/extract/main.nf index 499cac4bb77..f5b686db25f 100644 --- a/tests/modules/nf-core/methyldackel/extract/main.nf +++ b/tests/modules/nf-core/methyldackel/extract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { METHYLDACKEL_EXTRACT } from '../../../../modules/nf-core/methyldackel/extract/main.nf' +include { METHYLDACKEL_EXTRACT } from '../../../../../modules/nf-core/methyldackel/extract/main.nf' workflow test_methyldackel_extract { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/methyldackel/mbias/main.nf b/tests/modules/nf-core/methyldackel/mbias/main.nf index 99e5f1dfede..49c08b9f2c3 100644 --- a/tests/modules/nf-core/methyldackel/mbias/main.nf +++ b/tests/modules/nf-core/methyldackel/mbias/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { METHYLDACKEL_MBIAS } from '../../../../modules/nf-core/methyldackel/mbias/main.nf' +include { METHYLDACKEL_MBIAS } from '../../../../../modules/nf-core/methyldackel/mbias/main.nf' workflow test_methyldackel_mbias { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/minia/main.nf b/tests/modules/nf-core/minia/main.nf index 659f4dec787..a2e73a91927 100644 --- a/tests/modules/nf-core/minia/main.nf +++ b/tests/modules/nf-core/minia/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIA } from '../../../modules/nf-core/minia/main.nf' +include { MINIA } from '../../../../modules/nf-core/minia/main.nf' workflow test_minia { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/miniasm/main.nf b/tests/modules/nf-core/miniasm/main.nf index bbb6bffc0bb..5bc2a33416f 100644 --- a/tests/modules/nf-core/miniasm/main.nf +++ b/tests/modules/nf-core/miniasm/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIASM } from '../../../modules/nf-core/miniasm/main.nf' +include { MINIASM } from '../../../../modules/nf-core/miniasm/main.nf' workflow test_miniasm { diff --git a/tests/modules/nf-core/minimap2/align/main.nf b/tests/modules/nf-core/minimap2/align/main.nf index 6866ad349a1..c956d2301c7 100644 --- a/tests/modules/nf-core/minimap2/align/main.nf +++ b/tests/modules/nf-core/minimap2/align/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIMAP2_ALIGN } from '../../../../modules/nf-core/minimap2/align/main.nf' +include { MINIMAP2_ALIGN } from '../../../../../modules/nf-core/minimap2/align/main.nf' workflow test_minimap2_align_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/minimap2/index/main.nf b/tests/modules/nf-core/minimap2/index/main.nf index ac0dabc4964..212bb64e0ee 100644 --- a/tests/modules/nf-core/minimap2/index/main.nf +++ b/tests/modules/nf-core/minimap2/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MINIMAP2_INDEX } from '../../../../modules/nf-core/minimap2/index/main.nf' +include { MINIMAP2_INDEX } from '../../../../../modules/nf-core/minimap2/index/main.nf' workflow test_minimap2_index { diff --git a/tests/modules/nf-core/mlst/main.nf b/tests/modules/nf-core/mlst/main.nf index d924d06a707..863dc6b3ca2 100644 --- a/tests/modules/nf-core/mlst/main.nf +++ b/tests/modules/nf-core/mlst/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MLST } from '../../../modules/nf-core/mlst/main.nf' +include { MLST } from '../../../../modules/nf-core/mlst/main.nf' workflow test_mlst { diff --git a/tests/modules/nf-core/mobsuite/recon/main.nf b/tests/modules/nf-core/mobsuite/recon/main.nf index eb53a20bf97..cd04e1cb029 100644 --- a/tests/modules/nf-core/mobsuite/recon/main.nf +++ b/tests/modules/nf-core/mobsuite/recon/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MOBSUITE_RECON } from '../../../../modules/nf-core/mobsuite/recon/main.nf' +include { MOBSUITE_RECON } from '../../../../../modules/nf-core/mobsuite/recon/main.nf' workflow test_mobsuite_recon { diff --git a/tests/modules/nf-core/mosdepth/main.nf b/tests/modules/nf-core/mosdepth/main.nf index 20797307277..60b0e6cdb69 100644 --- a/tests/modules/nf-core/mosdepth/main.nf +++ b/tests/modules/nf-core/mosdepth/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/nf-core/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/nf-core/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../modules/nf-core/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH } from '../../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../../modules/nf-core/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../../modules/nf-core/mosdepth/main.nf' workflow test_mosdepth { input = [ diff --git a/tests/modules/nf-core/motus/downloaddb/main.nf b/tests/modules/nf-core/motus/downloaddb/main.nf index 328d957e506..0331beb85d1 100644 --- a/tests/modules/nf-core/motus/downloaddb/main.nf +++ b/tests/modules/nf-core/motus/downloaddb/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MOTUS_DOWNLOADDB } from '../../../../modules/nf-core/motus/downloaddb/main.nf' +include { MOTUS_DOWNLOADDB } from '../../../../../modules/nf-core/motus/downloaddb/main.nf' workflow test_motus_downloaddb { diff --git a/tests/modules/nf-core/motus/merge/main.nf b/tests/modules/nf-core/motus/merge/main.nf index d46546e71c8..22260b3f433 100644 --- a/tests/modules/nf-core/motus/merge/main.nf +++ b/tests/modules/nf-core/motus/merge/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { MOTUS_DOWNLOADDB } from '../../../../modules/nf-core/motus/downloaddb/main.nf' -include { MOTUS_PROFILE } from '../../../../modules/nf-core/motus/profile/main.nf' -include { MOTUS_MERGE } from '../../../../modules/nf-core/motus/merge/main.nf' -include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../modules/nf-core/motus/merge/main.nf' +include { MOTUS_DOWNLOADDB } from '../../../../../modules/nf-core/motus/downloaddb/main.nf' +include { MOTUS_PROFILE } from '../../../../../modules/nf-core/motus/profile/main.nf' +include { MOTUS_MERGE } from '../../../../../modules/nf-core/motus/merge/main.nf' +include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../../modules/nf-core/motus/merge/main.nf' workflow test_motus_merge { diff --git a/tests/modules/nf-core/motus/profile/main.nf b/tests/modules/nf-core/motus/profile/main.nf index 8c1eb873561..1add4dcf903 100644 --- a/tests/modules/nf-core/motus/profile/main.nf +++ b/tests/modules/nf-core/motus/profile/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MOTUS_DOWNLOADDB } from '../../../../modules/nf-core/motus/downloaddb/main.nf' -include { MOTUS_PROFILE } from '../../../../modules/nf-core/motus/profile/main.nf' +include { MOTUS_DOWNLOADDB } from '../../../../../modules/nf-core/motus/downloaddb/main.nf' +include { MOTUS_PROFILE } from '../../../../../modules/nf-core/motus/profile/main.nf' workflow test_motus_profile_single_end { diff --git a/tests/modules/nf-core/msisensor/msi/main.nf b/tests/modules/nf-core/msisensor/msi/main.nf index 4be59d25ea8..5d052c5b9c5 100644 --- a/tests/modules/nf-core/msisensor/msi/main.nf +++ b/tests/modules/nf-core/msisensor/msi/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MSISENSOR_SCAN } from '../../../../modules/nf-core/msisensor/scan/main.nf' -include { MSISENSOR_MSI } from '../../../../modules/nf-core/msisensor/msi/main.nf' +include { MSISENSOR_SCAN } from '../../../../../modules/nf-core/msisensor/scan/main.nf' +include { MSISENSOR_MSI } from '../../../../../modules/nf-core/msisensor/msi/main.nf' workflow test_msisensor_msi { diff --git a/tests/modules/nf-core/msisensor/scan/main.nf b/tests/modules/nf-core/msisensor/scan/main.nf index 2fb73c705a1..6b6383db1f3 100644 --- a/tests/modules/nf-core/msisensor/scan/main.nf +++ b/tests/modules/nf-core/msisensor/scan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MSISENSOR_SCAN } from '../../../../modules/nf-core/msisensor/scan/main.nf' +include { MSISENSOR_SCAN } from '../../../../../modules/nf-core/msisensor/scan/main.nf' workflow test_msisensor_scan { diff --git a/tests/modules/nf-core/msisensor2/msi/main.nf b/tests/modules/nf-core/msisensor2/msi/main.nf index 0c5b335f249..78738d27f67 100644 --- a/tests/modules/nf-core/msisensor2/msi/main.nf +++ b/tests/modules/nf-core/msisensor2/msi/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MSISENSOR2_SCAN } from '../../../../modules/nf-core/msisensor2/scan/main.nf' -include { MSISENSOR2_MSI } from '../../../../modules/nf-core/msisensor2/msi/main.nf' +include { MSISENSOR2_SCAN } from '../../../../../modules/nf-core/msisensor2/scan/main.nf' +include { MSISENSOR2_MSI } from '../../../../../modules/nf-core/msisensor2/msi/main.nf' workflow test_msisensor2_msi_tumor_only { diff --git a/tests/modules/nf-core/msisensor2/scan/main.nf b/tests/modules/nf-core/msisensor2/scan/main.nf index 2f92f82c5d3..a5bc912f776 100644 --- a/tests/modules/nf-core/msisensor2/scan/main.nf +++ b/tests/modules/nf-core/msisensor2/scan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MSISENSOR2_SCAN } from '../../../../modules/nf-core/msisensor2/scan/main.nf' +include { MSISENSOR2_SCAN } from '../../../../../modules/nf-core/msisensor2/scan/main.nf' workflow test_msisensor2_scan { diff --git a/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf b/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf index 8a78998f7c8..ed0a9d6f70c 100644 --- a/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/tests/modules/nf-core/msisensorpro/msi_somatic/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MSISENSORPRO_MSI_SOMATIC } from '../../../../modules/nf-core/msisensorpro/msi_somatic/main.nf' -include { MSISENSORPRO_SCAN } from '../../../../modules/nf-core/msisensorpro/scan/main.nf' +include { MSISENSORPRO_MSI_SOMATIC } from '../../../../../modules/nf-core/msisensorpro/msi_somatic/main.nf' +include { MSISENSORPRO_SCAN } from '../../../../../modules/nf-core/msisensorpro/scan/main.nf' workflow test_msisensorpro_msi { diff --git a/tests/modules/nf-core/msisensorpro/scan/main.nf b/tests/modules/nf-core/msisensorpro/scan/main.nf index 8413c662806..9647dc36ffb 100644 --- a/tests/modules/nf-core/msisensorpro/scan/main.nf +++ b/tests/modules/nf-core/msisensorpro/scan/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MSISENSORPRO_SCAN } from '../../../../modules/nf-core/msisensorpro/scan/main.nf' +include { MSISENSORPRO_SCAN } from '../../../../../modules/nf-core/msisensorpro/scan/main.nf' workflow test_msisensorpro_scan { diff --git a/tests/modules/nf-core/mtnucratio/main.nf b/tests/modules/nf-core/mtnucratio/main.nf index ee7d1572cb2..080210ee600 100644 --- a/tests/modules/nf-core/mtnucratio/main.nf +++ b/tests/modules/nf-core/mtnucratio/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MTNUCRATIO } from '../../../modules/nf-core/mtnucratio/main.nf' +include { MTNUCRATIO } from '../../../../modules/nf-core/mtnucratio/main.nf' workflow test_mtnucratio { diff --git a/tests/modules/nf-core/multiqc/main.nf b/tests/modules/nf-core/multiqc/main.nf index 640240a0cb1..f8ea220ca5e 100644 --- a/tests/modules/nf-core/multiqc/main.nf +++ b/tests/modules/nf-core/multiqc/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { FASTQC } from '../../../modules/nf-core/fastqc/main.nf' -include { FASTQC as FASTQC2 } from '../../../modules/nf-core/fastqc/main.nf' -include { MULTIQC } from '../../../modules/nf-core/multiqc/main.nf' +include { FASTQC } from '../../../../modules/nf-core/fastqc/main.nf' +include { FASTQC as FASTQC2 } from '../../../../modules/nf-core/fastqc/main.nf' +include { MULTIQC } from '../../../../modules/nf-core/multiqc/main.nf' workflow test_multiqc { input = [ diff --git a/tests/modules/nf-core/multivcfanalyzer/main.nf b/tests/modules/nf-core/multivcfanalyzer/main.nf index 92915fdc113..11bfd415c85 100644 --- a/tests/modules/nf-core/multivcfanalyzer/main.nf +++ b/tests/modules/nf-core/multivcfanalyzer/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { GATK_UNIFIEDGENOTYPER } from '../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' -include { GUNZIP } from '../../../modules/nf-core/gunzip/main.nf' -include { MULTIVCFANALYZER } from '../../../modules/nf-core/multivcfanalyzer/main.nf' +include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf' +include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' +include { MULTIVCFANALYZER } from '../../../../modules/nf-core/multivcfanalyzer/main.nf' workflow test_multivcfanalyzer { diff --git a/tests/modules/nf-core/mummer/main.nf b/tests/modules/nf-core/mummer/main.nf index ce7bbc661b5..68cfcfceb9d 100644 --- a/tests/modules/nf-core/mummer/main.nf +++ b/tests/modules/nf-core/mummer/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MUMMER } from '../../../modules/nf-core/mummer/main.nf' +include { MUMMER } from '../../../../modules/nf-core/mummer/main.nf' workflow test_mummer { diff --git a/tests/modules/nf-core/muscle/main.nf b/tests/modules/nf-core/muscle/main.nf index 0655f90a203..06759966b23 100644 --- a/tests/modules/nf-core/muscle/main.nf +++ b/tests/modules/nf-core/muscle/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { MUSCLE } from '../../../modules/nf-core/muscle/main.nf' -include { MUSCLE as MUSCLE_TREE } from '../../../modules/nf-core/muscle/main.nf' +include { MUSCLE } from '../../../../modules/nf-core/muscle/main.nf' +include { MUSCLE as MUSCLE_TREE } from '../../../../modules/nf-core/muscle/main.nf' workflow test_muscle { diff --git a/tests/modules/nf-core/mykrobe/predict/main.nf b/tests/modules/nf-core/mykrobe/predict/main.nf index 7c37a7532f6..6fbe60c36a5 100644 --- a/tests/modules/nf-core/mykrobe/predict/main.nf +++ b/tests/modules/nf-core/mykrobe/predict/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { MYKROBE_PREDICT } from '../../../../modules/nf-core/mykrobe/predict/main.nf' +include { MYKROBE_PREDICT } from '../../../../../modules/nf-core/mykrobe/predict/main.nf' workflow test_mykrobe_predict { diff --git a/tests/modules/nf-core/nanolyse/main.nf b/tests/modules/nf-core/nanolyse/main.nf index ef4cd33980d..a5ed562f2cb 100644 --- a/tests/modules/nf-core/nanolyse/main.nf +++ b/tests/modules/nf-core/nanolyse/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NANOLYSE } from '../../../modules/nf-core/nanolyse/main.nf' +include { NANOLYSE } from '../../../../modules/nf-core/nanolyse/main.nf' workflow test_nanolyse { input = [ diff --git a/tests/modules/nf-core/nanoplot/main.nf b/tests/modules/nf-core/nanoplot/main.nf index 395854171d6..e5e2bd59f6e 100644 --- a/tests/modules/nf-core/nanoplot/main.nf +++ b/tests/modules/nf-core/nanoplot/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NANOPLOT } from '../../../modules/nf-core/nanoplot/main.nf' +include { NANOPLOT } from '../../../../modules/nf-core/nanoplot/main.nf' workflow test_nanoplot_summary { def input = [] diff --git a/tests/modules/nf-core/ncbigenomedownload/main.nf b/tests/modules/nf-core/ncbigenomedownload/main.nf index cb32ad285e3..63a41517e46 100644 --- a/tests/modules/nf-core/ncbigenomedownload/main.nf +++ b/tests/modules/nf-core/ncbigenomedownload/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NCBIGENOMEDOWNLOAD } from '../../../modules/nf-core/ncbigenomedownload/main.nf' +include { NCBIGENOMEDOWNLOAD } from '../../../../modules/nf-core/ncbigenomedownload/main.nf' workflow test_ncbigenomedownload { diff --git a/tests/modules/nf-core/nextclade/datasetget/main.nf b/tests/modules/nf-core/nextclade/datasetget/main.nf index 4b1033f04ab..5935f8bbaaf 100644 --- a/tests/modules/nf-core/nextclade/datasetget/main.nf +++ b/tests/modules/nf-core/nextclade/datasetget/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NEXTCLADE_DATASETGET } from '../../../../modules/nf-core/nextclade/datasetget/main.nf' +include { NEXTCLADE_DATASETGET } from '../../../../../modules/nf-core/nextclade/datasetget/main.nf' workflow test_nextclade_datasetget { diff --git a/tests/modules/nf-core/nextclade/run/main.nf b/tests/modules/nf-core/nextclade/run/main.nf index 5288e4874d8..5c44ea4e7f3 100644 --- a/tests/modules/nf-core/nextclade/run/main.nf +++ b/tests/modules/nf-core/nextclade/run/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { NEXTCLADE_DATASETGET } from '../../../../modules/nf-core/nextclade/datasetget/main.nf' -include { NEXTCLADE_RUN } from '../../../../modules/nf-core/nextclade/run/main.nf' +include { NEXTCLADE_DATASETGET } from '../../../../../modules/nf-core/nextclade/datasetget/main.nf' +include { NEXTCLADE_RUN } from '../../../../../modules/nf-core/nextclade/run/main.nf' workflow test_nextclade_run { diff --git a/tests/modules/nf-core/nextgenmap/main.nf b/tests/modules/nf-core/nextgenmap/main.nf index d1ed609247c..89db132e2b0 100644 --- a/tests/modules/nf-core/nextgenmap/main.nf +++ b/tests/modules/nf-core/nextgenmap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NEXTGENMAP } from '../../../modules/nf-core/nextgenmap/main.nf' +include { NEXTGENMAP } from '../../../../modules/nf-core/nextgenmap/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/ngmaster/main.nf b/tests/modules/nf-core/ngmaster/main.nf index b3b2f27da4a..a6d4c12f19d 100644 --- a/tests/modules/nf-core/ngmaster/main.nf +++ b/tests/modules/nf-core/ngmaster/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NGMASTER } from '../../../modules/nf-core/ngmaster/main.nf' +include { NGMASTER } from '../../../../modules/nf-core/ngmaster/main.nf' workflow test_ngmaster { diff --git a/tests/modules/nf-core/ngscheckmate/ncm/main.nf b/tests/modules/nf-core/ngscheckmate/ncm/main.nf index 9b7bddd7560..00025215095 100644 --- a/tests/modules/nf-core/ngscheckmate/ncm/main.nf +++ b/tests/modules/nf-core/ngscheckmate/ncm/main.nf @@ -2,13 +2,13 @@ nextflow.enable.dsl = 2 -include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../modules/nf-core/ngscheckmate/ncm/main.nf' -include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../modules/nf-core/ngscheckmate/ncm/main.nf' +include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../../modules/nf-core/ngscheckmate/ncm/main.nf' +include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../../modules/nf-core/ngscheckmate/ncm/main.nf' -include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/nf-core/bedtools/makewindows/main.nf' +include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf' -include { BCFTOOLS_MPILEUP } from '../../../../modules/nf-core/bcftools/mpileup/main.nf' -include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../modules/nf-core/bcftools/mpileup/main.nf' +include { BCFTOOLS_MPILEUP } from '../../../../../modules/nf-core/bcftools/mpileup/main.nf' +include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../../modules/nf-core/bcftools/mpileup/main.nf' workflow test_ngscheckmate_ncm_bam { input = [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), diff --git a/tests/modules/nf-core/nucmer/main.nf b/tests/modules/nf-core/nucmer/main.nf index df9d3aedbeb..0799c7ff375 100644 --- a/tests/modules/nf-core/nucmer/main.nf +++ b/tests/modules/nf-core/nucmer/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { NUCMER } from '../../../modules/nf-core/nucmer/main.nf' +include { NUCMER } from '../../../../modules/nf-core/nucmer/main.nf' workflow test_nucmer { diff --git a/tests/modules/nf-core/optitype/main.nf b/tests/modules/nf-core/optitype/main.nf index c1a31718ecd..7771f682fb0 100644 --- a/tests/modules/nf-core/optitype/main.nf +++ b/tests/modules/nf-core/optitype/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { OPTITYPE } from '../../../modules/nf-core/optitype/main.nf' +include { OPTITYPE } from '../../../../modules/nf-core/optitype/main.nf' workflow test_optitype { input = [ [ id:'test', seq_type:'dna' ], // meta map diff --git a/tests/modules/nf-core/pairix/main.nf b/tests/modules/nf-core/pairix/main.nf index e54c90b2d40..04591eaf0c3 100644 --- a/tests/modules/nf-core/pairix/main.nf +++ b/tests/modules/nf-core/pairix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRIX } from '../../../modules/nf-core/pairix/main.nf' +include { PAIRIX } from '../../../../modules/nf-core/pairix/main.nf' workflow test_pairix { diff --git a/tests/modules/nf-core/pairtools/dedup/main.nf b/tests/modules/nf-core/pairtools/dedup/main.nf index 5735be4f529..6772b0bfe09 100644 --- a/tests/modules/nf-core/pairtools/dedup/main.nf +++ b/tests/modules/nf-core/pairtools/dedup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_DEDUP } from '../../../../modules/nf-core/pairtools/dedup/main.nf' +include { PAIRTOOLS_DEDUP } from '../../../../../modules/nf-core/pairtools/dedup/main.nf' workflow test_pairtools_dedup { diff --git a/tests/modules/nf-core/pairtools/flip/main.nf b/tests/modules/nf-core/pairtools/flip/main.nf index 0c3994f5b07..d891f6ae752 100644 --- a/tests/modules/nf-core/pairtools/flip/main.nf +++ b/tests/modules/nf-core/pairtools/flip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_FLIP } from '../../../../modules/nf-core/pairtools/flip/main.nf' +include { PAIRTOOLS_FLIP } from '../../../../../modules/nf-core/pairtools/flip/main.nf' workflow test_pairtools_flip { diff --git a/tests/modules/nf-core/pairtools/parse/main.nf b/tests/modules/nf-core/pairtools/parse/main.nf index 2ff878698db..4b387e1c4e1 100644 --- a/tests/modules/nf-core/pairtools/parse/main.nf +++ b/tests/modules/nf-core/pairtools/parse/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_PARSE } from '../../../../modules/nf-core/pairtools/parse/main.nf' +include { PAIRTOOLS_PARSE } from '../../../../../modules/nf-core/pairtools/parse/main.nf' workflow test_pairtools_parse { diff --git a/tests/modules/nf-core/pairtools/restrict/main.nf b/tests/modules/nf-core/pairtools/restrict/main.nf index ca36e9a45bb..62302473002 100644 --- a/tests/modules/nf-core/pairtools/restrict/main.nf +++ b/tests/modules/nf-core/pairtools/restrict/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_RESTRICT } from '../../../../modules/nf-core/pairtools/restrict/main.nf' +include { PAIRTOOLS_RESTRICT } from '../../../../../modules/nf-core/pairtools/restrict/main.nf' workflow test_pairtools_restrict { diff --git a/tests/modules/nf-core/pairtools/select/main.nf b/tests/modules/nf-core/pairtools/select/main.nf index 9b41bb74aa2..2eddb21bee4 100644 --- a/tests/modules/nf-core/pairtools/select/main.nf +++ b/tests/modules/nf-core/pairtools/select/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_SELECT } from '../../../../modules/nf-core/pairtools/select/main.nf' +include { PAIRTOOLS_SELECT } from '../../../../../modules/nf-core/pairtools/select/main.nf' workflow test_pairtools_select { diff --git a/tests/modules/nf-core/pairtools/sort/main.nf b/tests/modules/nf-core/pairtools/sort/main.nf index a5b77ca85f8..6ec22c67f91 100644 --- a/tests/modules/nf-core/pairtools/sort/main.nf +++ b/tests/modules/nf-core/pairtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PAIRTOOLS_SORT } from '../../../../modules/nf-core/pairtools/sort/main.nf' +include { PAIRTOOLS_SORT } from '../../../../../modules/nf-core/pairtools/sort/main.nf' workflow test_pairtools_sort { diff --git a/tests/modules/nf-core/panaroo/run/main.nf b/tests/modules/nf-core/panaroo/run/main.nf index fb0899b7843..ac7329bcd8f 100644 --- a/tests/modules/nf-core/panaroo/run/main.nf +++ b/tests/modules/nf-core/panaroo/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PANAROO_RUN } from '../../../../modules/nf-core/panaroo/run/main.nf' +include { PANAROO_RUN } from '../../../../../modules/nf-core/panaroo/run/main.nf' workflow test_panaroo_run { diff --git a/tests/modules/nf-core/pangolin/main.nf b/tests/modules/nf-core/pangolin/main.nf index 9ee1995f76f..6bed60ae0d7 100644 --- a/tests/modules/nf-core/pangolin/main.nf +++ b/tests/modules/nf-core/pangolin/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PANGOLIN } from '../../../modules/nf-core/pangolin/main.nf' +include { PANGOLIN } from '../../../../modules/nf-core/pangolin/main.nf' workflow test_pangolin { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/paraclu/main.nf b/tests/modules/nf-core/paraclu/main.nf index 9f1ccf26f94..1e7b71382a5 100644 --- a/tests/modules/nf-core/paraclu/main.nf +++ b/tests/modules/nf-core/paraclu/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PARACLU } from '../../../modules/nf-core/paraclu/main.nf' +include { PARACLU } from '../../../../modules/nf-core/paraclu/main.nf' workflow test_paraclu { diff --git a/tests/modules/nf-core/pasty/main.nf b/tests/modules/nf-core/pasty/main.nf index 582e15997ec..d4e8f397a63 100644 --- a/tests/modules/nf-core/pasty/main.nf +++ b/tests/modules/nf-core/pasty/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PASTY } from '../../../modules/nf-core/pasty/main.nf' +include { PASTY } from '../../../../modules/nf-core/pasty/main.nf' workflow test_pasty { diff --git a/tests/modules/nf-core/pbbam/pbmerge/main.nf b/tests/modules/nf-core/pbbam/pbmerge/main.nf index af6330936b1..52334508896 100644 --- a/tests/modules/nf-core/pbbam/pbmerge/main.nf +++ b/tests/modules/nf-core/pbbam/pbmerge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PBBAM_PBMERGE } from '../../../../modules/nf-core/pbbam/pbmerge/main.nf' +include { PBBAM_PBMERGE } from '../../../../../modules/nf-core/pbbam/pbmerge/main.nf' workflow test_pbbam_pbmerge { diff --git a/tests/modules/nf-core/pbccs/main.nf b/tests/modules/nf-core/pbccs/main.nf index be09774ce32..17c8f8e0992 100644 --- a/tests/modules/nf-core/pbccs/main.nf +++ b/tests/modules/nf-core/pbccs/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PBCCS } from '../../../modules/nf-core/pbccs/main.nf' +include { PBCCS } from '../../../../modules/nf-core/pbccs/main.nf' workflow test_pbccs { diff --git a/tests/modules/nf-core/pbptyper/main.nf b/tests/modules/nf-core/pbptyper/main.nf index 706f5804ac2..39a310b9016 100644 --- a/tests/modules/nf-core/pbptyper/main.nf +++ b/tests/modules/nf-core/pbptyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PBPTYPER } from '../../../modules/nf-core/pbptyper/main.nf' +include { PBPTYPER } from '../../../../modules/nf-core/pbptyper/main.nf' workflow test_pbptyper { diff --git a/tests/modules/nf-core/pear/main.nf b/tests/modules/nf-core/pear/main.nf index f46e7789387..0b49c247479 100644 --- a/tests/modules/nf-core/pear/main.nf +++ b/tests/modules/nf-core/pear/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PEAR } from '../../../modules/nf-core/pear/main.nf' +include { PEAR } from '../../../../modules/nf-core/pear/main.nf' workflow test_pear { diff --git a/tests/modules/nf-core/peddy/main.nf b/tests/modules/nf-core/peddy/main.nf index 41821768834..c5a605fa2ad 100644 --- a/tests/modules/nf-core/peddy/main.nf +++ b/tests/modules/nf-core/peddy/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PEDDY } from '../../../modules/nf-core/peddy/main.nf' +include { PEDDY } from '../../../../modules/nf-core/peddy/main.nf' workflow test_peddy { diff --git a/tests/modules/nf-core/phantompeakqualtools/main.nf b/tests/modules/nf-core/phantompeakqualtools/main.nf index 7d91e3f156c..57ac3ac8c5c 100644 --- a/tests/modules/nf-core/phantompeakqualtools/main.nf +++ b/tests/modules/nf-core/phantompeakqualtools/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PHANTOMPEAKQUALTOOLS } from '../../../modules/nf-core/phantompeakqualtools/main.nf' +include { PHANTOMPEAKQUALTOOLS } from '../../../../modules/nf-core/phantompeakqualtools/main.nf' workflow test_phantompeakqualtools_single_end { diff --git a/tests/modules/nf-core/phyloflash/main.nf b/tests/modules/nf-core/phyloflash/main.nf index 18f2b1cae94..3e7549a676b 100644 --- a/tests/modules/nf-core/phyloflash/main.nf +++ b/tests/modules/nf-core/phyloflash/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PHYLOFLASH } from '../../../modules/nf-core/phyloflash/main.nf' +include { PHYLOFLASH } from '../../../../modules/nf-core/phyloflash/main.nf' process STUB_PHYLOFLASH_DATABASE { output: diff --git a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf index 71ae501d7fe..e0196f34016 100644 --- a/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/tests/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../modules/nf-core/picard/addorreplacereadgroups/main.nf' +include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../../modules/nf-core/picard/addorreplacereadgroups/main.nf' workflow test_picard_addorreplacereadgroups { diff --git a/tests/modules/nf-core/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf index c6f4a2d890b..d337aca51ee 100644 --- a/tests/modules/nf-core/picard/cleansam/main.nf +++ b/tests/modules/nf-core/picard/cleansam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_CLEANSAM } from '../../../../modules/nf-core/picard/cleansam/main.nf' +include { PICARD_CLEANSAM } from '../../../../../modules/nf-core/picard/cleansam/main.nf' workflow test_picard_cleansam { diff --git a/tests/modules/nf-core/picard/collecthsmetrics/main.nf b/tests/modules/nf-core/picard/collecthsmetrics/main.nf index 913d29e4621..2876353b047 100644 --- a/tests/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/tests/modules/nf-core/picard/collecthsmetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTHSMETRICS } from '../../../../modules/nf-core/picard/collecthsmetrics/main.nf' +include { PICARD_COLLECTHSMETRICS } from '../../../../../modules/nf-core/picard/collecthsmetrics/main.nf' workflow test_picard_collecthsmetrics { diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf index 4eb7d63b708..0271a293779 100644 --- a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/nf-core/picard/collectmultiplemetrics/main.nf' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../../modules/nf-core/picard/collectmultiplemetrics/main.nf' workflow test_picard_collectmultiplemetrics { input = [ diff --git a/tests/modules/nf-core/picard/collectwgsmetrics/main.nf b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf index 1e7fb9bff10..42ac40fb89e 100644 --- a/tests/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/tests/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/nf-core/picard/collectwgsmetrics/main.nf' +include { PICARD_COLLECTWGSMETRICS } from '../../../../../modules/nf-core/picard/collectwgsmetrics/main.nf' workflow test_picard_collectwgsmetrics { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/picard/createsequencedictionary/main.nf b/tests/modules/nf-core/picard/createsequencedictionary/main.nf index 9a678467f9e..fcdc50b641d 100644 --- a/tests/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/tests/modules/nf-core/picard/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../modules/nf-core/picard/createsequencedictionary/main.nf' +include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../../modules/nf-core/picard/createsequencedictionary/main.nf' workflow test_picard_createsequencedictionary { diff --git a/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf index d7c21662fae..bef0537205a 100644 --- a/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/tests/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../modules/nf-core/picard/crosscheckfingerprints/main.nf' +include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../../modules/nf-core/picard/crosscheckfingerprints/main.nf' workflow test_picard_crosscheckfingerprints { diff --git a/tests/modules/nf-core/picard/fastqtosam/main.nf b/tests/modules/nf-core/picard/fastqtosam/main.nf index e2b42ee53a9..5b1af7ea9fc 100644 --- a/tests/modules/nf-core/picard/fastqtosam/main.nf +++ b/tests/modules/nf-core/picard/fastqtosam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_FASTQTOSAM } from '../../../../modules/nf-core/picard/fastqtosam/main.nf' +include { PICARD_FASTQTOSAM } from '../../../../../modules/nf-core/picard/fastqtosam/main.nf' workflow test_picard_fastqtosam_single { diff --git a/tests/modules/nf-core/picard/filtersamreads/main.nf b/tests/modules/nf-core/picard/filtersamreads/main.nf index 9fe3e04b0b5..3687bbfb19b 100644 --- a/tests/modules/nf-core/picard/filtersamreads/main.nf +++ b/tests/modules/nf-core/picard/filtersamreads/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTSAM } from '../../../../modules/nf-core/picard/sortsam/main.nf' -include { PICARD_FILTERSAMREADS } from '../../../../modules/nf-core/picard/filtersamreads/main.nf' +include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf' +include { PICARD_FILTERSAMREADS } from '../../../../../modules/nf-core/picard/filtersamreads/main.nf' workflow test_picard_filtersamreads { diff --git a/tests/modules/nf-core/picard/fixmateinformation/main.nf b/tests/modules/nf-core/picard/fixmateinformation/main.nf index 0cdccd14e0e..92277611f29 100644 --- a/tests/modules/nf-core/picard/fixmateinformation/main.nf +++ b/tests/modules/nf-core/picard/fixmateinformation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_FIXMATEINFORMATION } from '../../../../modules/nf-core/picard/fixmateinformation/main.nf' +include { PICARD_FIXMATEINFORMATION } from '../../../../../modules/nf-core/picard/fixmateinformation/main.nf' workflow test_picard_fixmateinformation { diff --git a/tests/modules/nf-core/picard/liftovervcf/main.nf b/tests/modules/nf-core/picard/liftovervcf/main.nf index 20cff729b7e..94a78fbcd85 100644 --- a/tests/modules/nf-core/picard/liftovervcf/main.nf +++ b/tests/modules/nf-core/picard/liftovervcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_LIFTOVERVCF } from '../../../../modules/nf-core/picard/liftovervcf/main.nf' +include { PICARD_LIFTOVERVCF } from '../../../../../modules/nf-core/picard/liftovervcf/main.nf' workflow test_picard_liftovervcf { diff --git a/tests/modules/nf-core/picard/markduplicates/main.nf b/tests/modules/nf-core/picard/markduplicates/main.nf index 33ac5f55a35..941bec1ca41 100644 --- a/tests/modules/nf-core/picard/markduplicates/main.nf +++ b/tests/modules/nf-core/picard/markduplicates/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PICARD_MARKDUPLICATES } from '../../../../modules/nf-core/picard/markduplicates/main.nf' -include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/nf-core/picard/markduplicates/main.nf' +include { PICARD_MARKDUPLICATES } from '../../../../../modules/nf-core/picard/markduplicates/main.nf' +include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../../modules/nf-core/picard/markduplicates/main.nf' workflow test_picard_markduplicates_sorted_bam { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/picard/mergesamfiles/main.nf b/tests/modules/nf-core/picard/mergesamfiles/main.nf index a02e0656ede..360cfd7ed0d 100644 --- a/tests/modules/nf-core/picard/mergesamfiles/main.nf +++ b/tests/modules/nf-core/picard/mergesamfiles/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_MERGESAMFILES } from '../../../../modules/nf-core/picard/mergesamfiles/main.nf' +include { PICARD_MERGESAMFILES } from '../../../../../modules/nf-core/picard/mergesamfiles/main.nf' workflow test_picard_mergesamfiles { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf index 70f8a267419..4b4e801355a 100644 --- a/tests/modules/nf-core/picard/sortsam/main.nf +++ b/tests/modules/nf-core/picard/sortsam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTSAM } from '../../../../modules/nf-core/picard/sortsam/main.nf' +include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf' workflow test_picard_sortsam { diff --git a/tests/modules/nf-core/picard/sortvcf/main.nf b/tests/modules/nf-core/picard/sortvcf/main.nf index 0b56089e695..f4d9c391411 100644 --- a/tests/modules/nf-core/picard/sortvcf/main.nf +++ b/tests/modules/nf-core/picard/sortvcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PICARD_SORTVCF } from '../../../../modules/nf-core/picard/sortvcf/main.nf' +include { PICARD_SORTVCF } from '../../../../../modules/nf-core/picard/sortvcf/main.nf' workflow test_picard_sortvcf { diff --git a/tests/modules/nf-core/pints/caller/main.nf b/tests/modules/nf-core/pints/caller/main.nf index 0f69cda4191..a5cccca59f4 100644 --- a/tests/modules/nf-core/pints/caller/main.nf +++ b/tests/modules/nf-core/pints/caller/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PINTS_CALLER } from '../../../../modules/nf-core/pints/caller/main.nf' +include { PINTS_CALLER } from '../../../../../modules/nf-core/pints/caller/main.nf' workflow test_pints_caller { diff --git a/tests/modules/nf-core/pirate/main.nf b/tests/modules/nf-core/pirate/main.nf index 11c60f43295..0def80c4bfe 100644 --- a/tests/modules/nf-core/pirate/main.nf +++ b/tests/modules/nf-core/pirate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PIRATE } from '../../../modules/nf-core/pirate/main.nf' +include { PIRATE } from '../../../../modules/nf-core/pirate/main.nf' workflow test_pirate { diff --git a/tests/modules/nf-core/plasmidfinder/main.nf b/tests/modules/nf-core/plasmidfinder/main.nf index 08dd396e1ee..9b79e37310c 100644 --- a/tests/modules/nf-core/plasmidfinder/main.nf +++ b/tests/modules/nf-core/plasmidfinder/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLASMIDFINDER } from '../../../modules/nf-core/plasmidfinder/main.nf' +include { PLASMIDFINDER } from '../../../../modules/nf-core/plasmidfinder/main.nf' workflow test_plasmidfinder { diff --git a/tests/modules/nf-core/plasmidid/main.nf b/tests/modules/nf-core/plasmidid/main.nf index e47230828f8..4ef7fc64ac8 100644 --- a/tests/modules/nf-core/plasmidid/main.nf +++ b/tests/modules/nf-core/plasmidid/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLASMIDID } from '../../../modules/nf-core/plasmidid/main.nf' +include { PLASMIDID } from '../../../../modules/nf-core/plasmidid/main.nf' workflow test_plasmidid { diff --git a/tests/modules/nf-core/plink/extract/main.nf b/tests/modules/nf-core/plink/extract/main.nf index 806959b8d1b..f0a50a5ac49 100644 --- a/tests/modules/nf-core/plink/extract/main.nf +++ b/tests/modules/nf-core/plink/extract/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PLINK_VCF } from '../../../../modules/nf-core/plink/vcf/main.nf' -include { PLINK_EXTRACT } from '../../../../modules/nf-core/plink/extract/main.nf' +include { PLINK_VCF } from '../../../../../modules/nf-core/plink/vcf/main.nf' +include { PLINK_EXTRACT } from '../../../../../modules/nf-core/plink/extract/main.nf' workflow test_plink_extract { diff --git a/tests/modules/nf-core/plink/vcf/main.nf b/tests/modules/nf-core/plink/vcf/main.nf index 1cac7969f86..59119c238db 100644 --- a/tests/modules/nf-core/plink/vcf/main.nf +++ b/tests/modules/nf-core/plink/vcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLINK_VCF } from '../../../../modules/nf-core/plink/vcf/main.nf' +include { PLINK_VCF } from '../../../../../modules/nf-core/plink/vcf/main.nf' workflow test_plink_vcf { diff --git a/tests/modules/nf-core/plink2/extract/main.nf b/tests/modules/nf-core/plink2/extract/main.nf index 7f00ef29fd8..f442edb8f24 100644 --- a/tests/modules/nf-core/plink2/extract/main.nf +++ b/tests/modules/nf-core/plink2/extract/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PLINK2_VCF } from '../../../../modules/nf-core/plink2/vcf/main.nf' -include { PLINK2_EXTRACT } from '../../../../modules/nf-core/plink2/extract/main.nf' +include { PLINK2_VCF } from '../../../../../modules/nf-core/plink2/vcf/main.nf' +include { PLINK2_EXTRACT } from '../../../../../modules/nf-core/plink2/extract/main.nf' workflow test_plink2_extract { diff --git a/tests/modules/nf-core/plink2/score/main.nf b/tests/modules/nf-core/plink2/score/main.nf index f9a2692209d..75cedf22f5f 100644 --- a/tests/modules/nf-core/plink2/score/main.nf +++ b/tests/modules/nf-core/plink2/score/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PLINK2_VCF } from '../../../../modules/nf-core/plink2/vcf/main.nf' -include { PLINK2_SCORE } from '../../../../modules/nf-core/plink2/score/main.nf' +include { PLINK2_VCF } from '../../../../../modules/nf-core/plink2/vcf/main.nf' +include { PLINK2_SCORE } from '../../../../../modules/nf-core/plink2/score/main.nf' workflow test_plink2_score { input = [ diff --git a/tests/modules/nf-core/plink2/vcf/main.nf b/tests/modules/nf-core/plink2/vcf/main.nf index e417922b3b6..abdfb9b0bef 100644 --- a/tests/modules/nf-core/plink2/vcf/main.nf +++ b/tests/modules/nf-core/plink2/vcf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PLINK2_VCF } from '../../../../modules/nf-core/plink2/vcf/main.nf' +include { PLINK2_VCF } from '../../../../../modules/nf-core/plink2/vcf/main.nf' workflow test_plink2_vcf { diff --git a/tests/modules/nf-core/pmdtools/filter/main.nf b/tests/modules/nf-core/pmdtools/filter/main.nf index 6d9973e825a..5c8531b3e0f 100644 --- a/tests/modules/nf-core/pmdtools/filter/main.nf +++ b/tests/modules/nf-core/pmdtools/filter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PMDTOOLS_FILTER } from '../../../../modules/nf-core/pmdtools/filter/main.nf' +include { PMDTOOLS_FILTER } from '../../../../../modules/nf-core/pmdtools/filter/main.nf' workflow test_pmdtools_filter { diff --git a/tests/modules/nf-core/porechop/main.nf b/tests/modules/nf-core/porechop/main.nf index fb6ae0e7dd2..59f68c5c5d9 100644 --- a/tests/modules/nf-core/porechop/main.nf +++ b/tests/modules/nf-core/porechop/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PORECHOP } from '../../../modules/nf-core/porechop/main.nf' +include { PORECHOP } from '../../../../modules/nf-core/porechop/main.nf' workflow test_porechop { diff --git a/tests/modules/nf-core/preseq/ccurve/main.nf b/tests/modules/nf-core/preseq/ccurve/main.nf index 1c03a1eb87e..cee8a6c52bb 100644 --- a/tests/modules/nf-core/preseq/ccurve/main.nf +++ b/tests/modules/nf-core/preseq/ccurve/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRESEQ_CCURVE } from '../../../../modules/nf-core/preseq/ccurve/main.nf' +include { PRESEQ_CCURVE } from '../../../../../modules/nf-core/preseq/ccurve/main.nf' workflow test_preseq_ccurve_single_end { diff --git a/tests/modules/nf-core/preseq/lcextrap/main.nf b/tests/modules/nf-core/preseq/lcextrap/main.nf index 24028337dcf..be87f23362c 100644 --- a/tests/modules/nf-core/preseq/lcextrap/main.nf +++ b/tests/modules/nf-core/preseq/lcextrap/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRESEQ_LCEXTRAP } from '../../../../modules/nf-core/preseq/lcextrap/main.nf' +include { PRESEQ_LCEXTRAP } from '../../../../../modules/nf-core/preseq/lcextrap/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/prinseqplusplus/main.nf b/tests/modules/nf-core/prinseqplusplus/main.nf index 2b162110967..b604b8091ec 100644 --- a/tests/modules/nf-core/prinseqplusplus/main.nf +++ b/tests/modules/nf-core/prinseqplusplus/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRINSEQPLUSPLUS } from '../../../modules/nf-core/prinseqplusplus/main.nf' +include { PRINSEQPLUSPLUS } from '../../../../modules/nf-core/prinseqplusplus/main.nf' workflow test_prinseqplusplus_single_end { diff --git a/tests/modules/nf-core/prodigal/main.nf b/tests/modules/nf-core/prodigal/main.nf index fcbff592a39..c69f887e5fa 100644 --- a/tests/modules/nf-core/prodigal/main.nf +++ b/tests/modules/nf-core/prodigal/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PRODIGAL } from '../../../modules/nf-core/prodigal/main.nf' +include { PRODIGAL } from '../../../../modules/nf-core/prodigal/main.nf' workflow test_prodigal { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/prokka/main.nf b/tests/modules/nf-core/prokka/main.nf index 8b2380da35f..ff17e956831 100644 --- a/tests/modules/nf-core/prokka/main.nf +++ b/tests/modules/nf-core/prokka/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PROKKA } from '../../../modules/nf-core/prokka/main.nf' +include { PROKKA } from '../../../../modules/nf-core/prokka/main.nf' workflow test_prokka { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/pycoqc/main.nf b/tests/modules/nf-core/pycoqc/main.nf index 2e2ddd3c4b0..8256d3f1350 100644 --- a/tests/modules/nf-core/pycoqc/main.nf +++ b/tests/modules/nf-core/pycoqc/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PYCOQC } from '../../../modules/nf-core/pycoqc/main.nf' +include { PYCOQC } from '../../../../modules/nf-core/pycoqc/main.nf' workflow test_pycoqc { diff --git a/tests/modules/nf-core/pydamage/analyze/main.nf b/tests/modules/nf-core/pydamage/analyze/main.nf index ea67412dc65..786eb11622b 100644 --- a/tests/modules/nf-core/pydamage/analyze/main.nf +++ b/tests/modules/nf-core/pydamage/analyze/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { PYDAMAGE_ANALYZE } from '../../../../modules/nf-core/pydamage/analyze/main.nf' +include { PYDAMAGE_ANALYZE } from '../../../../../modules/nf-core/pydamage/analyze/main.nf' workflow test_pydamage { diff --git a/tests/modules/nf-core/pydamage/filter/main.nf b/tests/modules/nf-core/pydamage/filter/main.nf index dd0d2588447..bc2d1e30bf4 100644 --- a/tests/modules/nf-core/pydamage/filter/main.nf +++ b/tests/modules/nf-core/pydamage/filter/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { PYDAMAGE_ANALYZE } from '../../../../modules/nf-core/pydamage/analyze/main.nf' -include { PYDAMAGE_FILTER } from '../../../../modules/nf-core/pydamage/filter/main.nf' +include { PYDAMAGE_ANALYZE } from '../../../../../modules/nf-core/pydamage/analyze/main.nf' +include { PYDAMAGE_FILTER } from '../../../../../modules/nf-core/pydamage/filter/main.nf' workflow test_pydamage { diff --git a/tests/modules/nf-core/qcat/main.nf b/tests/modules/nf-core/qcat/main.nf index 196e54e6674..c64d6367a66 100644 --- a/tests/modules/nf-core/qcat/main.nf +++ b/tests/modules/nf-core/qcat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QCAT } from '../../../modules/nf-core/qcat/main.nf' +include { QCAT } from '../../../../modules/nf-core/qcat/main.nf' workflow test_qcat { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/qualimap/bamqc/main.nf b/tests/modules/nf-core/qualimap/bamqc/main.nf index bfd61ff38ae..f3f6b8c16fc 100644 --- a/tests/modules/nf-core/qualimap/bamqc/main.nf +++ b/tests/modules/nf-core/qualimap/bamqc/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QUALIMAP_BAMQC } from '../../../../modules/nf-core/qualimap/bamqc/main.nf' +include { QUALIMAP_BAMQC } from '../../../../../modules/nf-core/qualimap/bamqc/main.nf' workflow test_qualimap_bamqc { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/qualimap/bamqccram/main.nf b/tests/modules/nf-core/qualimap/bamqccram/main.nf index b1b7c0ea5a6..cd375985414 100644 --- a/tests/modules/nf-core/qualimap/bamqccram/main.nf +++ b/tests/modules/nf-core/qualimap/bamqccram/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QUALIMAP_BAMQCCRAM } from '../../../../modules/nf-core/qualimap/bamqccram/main.nf' +include { QUALIMAP_BAMQCCRAM } from '../../../../../modules/nf-core/qualimap/bamqccram/main.nf' workflow test_qualimap_bamqc { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/quast/main.nf b/tests/modules/nf-core/quast/main.nf index fc99bd494f9..58377d43e2d 100644 --- a/tests/modules/nf-core/quast/main.nf +++ b/tests/modules/nf-core/quast/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { QUAST } from '../../../modules/nf-core/quast/main.nf' +include { QUAST } from '../../../../modules/nf-core/quast/main.nf' workflow test_quast_ref { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/racon/main.nf b/tests/modules/nf-core/racon/main.nf index 37812aacca3..416e498be99 100644 --- a/tests/modules/nf-core/racon/main.nf +++ b/tests/modules/nf-core/racon/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RACON } from '../../../modules/nf-core/racon/main.nf' +include { RACON } from '../../../../modules/nf-core/racon/main.nf' workflow test_racon { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/rapidnj/main.nf b/tests/modules/nf-core/rapidnj/main.nf index b3209a67df5..af9caac2f95 100644 --- a/tests/modules/nf-core/rapidnj/main.nf +++ b/tests/modules/nf-core/rapidnj/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RAPIDNJ } from '../../../modules/nf-core/rapidnj/main.nf' +include { RAPIDNJ } from '../../../../modules/nf-core/rapidnj/main.nf' workflow test_rapidnj { diff --git a/tests/modules/nf-core/rasusa/main.nf b/tests/modules/nf-core/rasusa/main.nf index 48120746e11..d8ffdb74d06 100644 --- a/tests/modules/nf-core/rasusa/main.nf +++ b/tests/modules/nf-core/rasusa/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RASUSA } from '../../../modules/nf-core/rasusa/main.nf' +include { RASUSA } from '../../../../modules/nf-core/rasusa/main.nf' workflow test_rasusa { input = [ [ id:'test', single_end:false], // meta map diff --git a/tests/modules/nf-core/raven/main.nf b/tests/modules/nf-core/raven/main.nf index a126158d8ec..d354c209583 100644 --- a/tests/modules/nf-core/raven/main.nf +++ b/tests/modules/nf-core/raven/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RAVEN } from '../../../modules/nf-core/raven/main.nf' +include { RAVEN } from '../../../../modules/nf-core/raven/main.nf' workflow test_raven { diff --git a/tests/modules/nf-core/raxmlng/main.nf b/tests/modules/nf-core/raxmlng/main.nf index 8450af59865..78f1107fcec 100644 --- a/tests/modules/nf-core/raxmlng/main.nf +++ b/tests/modules/nf-core/raxmlng/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../modules/nf-core/raxmlng/main.nf' -include { RAXMLNG as RAXMLNG_BOOTSTRAP } from '../../../modules/nf-core/raxmlng/main.nf' +include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../../modules/nf-core/raxmlng/main.nf' +include { RAXMLNG as RAXMLNG_BOOTSTRAP } from '../../../../modules/nf-core/raxmlng/main.nf' // // Test without bootstrapping diff --git a/tests/modules/nf-core/rgi/main/main.nf b/tests/modules/nf-core/rgi/main/main.nf index b30c83403e9..f1cd67fe5cc 100644 --- a/tests/modules/nf-core/rgi/main/main.nf +++ b/tests/modules/nf-core/rgi/main/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RGI_MAIN } from '../../../../modules/nf-core/rgi/main/main.nf' +include { RGI_MAIN } from '../../../../../modules/nf-core/rgi/main/main.nf' workflow test_rgi_main { diff --git a/tests/modules/nf-core/rhocall/annotate/main.nf b/tests/modules/nf-core/rhocall/annotate/main.nf index fcc156d3997..9dd7c01414e 100644 --- a/tests/modules/nf-core/rhocall/annotate/main.nf +++ b/tests/modules/nf-core/rhocall/annotate/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RHOCALL_ANNOTATE } from '../../../../modules/nf-core/rhocall/annotate/main.nf' -include { BCFTOOLS_ROH } from '../../../../modules/nf-core/bcftools/roh/main.nf' +include { RHOCALL_ANNOTATE } from '../../../../../modules/nf-core/rhocall/annotate/main.nf' +include { BCFTOOLS_ROH } from '../../../../../modules/nf-core/bcftools/roh/main.nf' workflow test_rhocall_annotate { diff --git a/tests/modules/nf-core/rmarkdownnotebook/main.nf b/tests/modules/nf-core/rmarkdownnotebook/main.nf index 4b1777a2e21..6e628854bf1 100644 --- a/tests/modules/nf-core/rmarkdownnotebook/main.nf +++ b/tests/modules/nf-core/rmarkdownnotebook/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RMARKDOWNNOTEBOOK } from '../../../modules/nf-core/rmarkdownnotebook/main.nf' -include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/nf-core/rmarkdownnotebook/main.nf' +include { RMARKDOWNNOTEBOOK } from '../../../../modules/nf-core/rmarkdownnotebook/main.nf' +include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../../modules/nf-core/rmarkdownnotebook/main.nf' workflow test_rmarkdown { diff --git a/tests/modules/nf-core/roary/main.nf b/tests/modules/nf-core/roary/main.nf index 07d896fbada..4fd915a09d7 100644 --- a/tests/modules/nf-core/roary/main.nf +++ b/tests/modules/nf-core/roary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ROARY } from '../../../modules/nf-core/roary/main.nf' +include { ROARY } from '../../../../modules/nf-core/roary/main.nf' workflow test_roary { diff --git a/tests/modules/nf-core/rsem/calculateexpression/main.nf b/tests/modules/nf-core/rsem/calculateexpression/main.nf index 57d9249ce86..d4989d64423 100644 --- a/tests/modules/nf-core/rsem/calculateexpression/main.nf +++ b/tests/modules/nf-core/rsem/calculateexpression/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RSEM_PREPAREREFERENCE } from '../../../../modules/nf-core/rsem/preparereference/main.nf' -include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/nf-core/rsem/calculateexpression/main.nf' +include { RSEM_PREPAREREFERENCE } from '../../../../../modules/nf-core/rsem/preparereference/main.nf' +include { RSEM_CALCULATEEXPRESSION } from '../../../../../modules/nf-core/rsem/calculateexpression/main.nf' workflow test_rsem_calculateexpression { diff --git a/tests/modules/nf-core/rsem/preparereference/main.nf b/tests/modules/nf-core/rsem/preparereference/main.nf index 276fa74a2f5..4b1e409491e 100644 --- a/tests/modules/nf-core/rsem/preparereference/main.nf +++ b/tests/modules/nf-core/rsem/preparereference/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEM_PREPAREREFERENCE } from '../../../../modules/nf-core/rsem/preparereference/main.nf' +include { RSEM_PREPAREREFERENCE } from '../../../../../modules/nf-core/rsem/preparereference/main.nf' workflow test_rsem_preparereference { diff --git a/tests/modules/nf-core/rseqc/bamstat/main.nf b/tests/modules/nf-core/rseqc/bamstat/main.nf index d2c4c779014..489d5b5cdab 100644 --- a/tests/modules/nf-core/rseqc/bamstat/main.nf +++ b/tests/modules/nf-core/rseqc/bamstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_BAMSTAT } from '../../../../modules/nf-core/rseqc/bamstat/main.nf' +include { RSEQC_BAMSTAT } from '../../../../../modules/nf-core/rseqc/bamstat/main.nf' workflow test_rseqc_bamstat { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/rseqc/inferexperiment/main.nf b/tests/modules/nf-core/rseqc/inferexperiment/main.nf index 043fd01973f..65f358107fb 100644 --- a/tests/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/tests/modules/nf-core/rseqc/inferexperiment/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_INFEREXPERIMENT } from '../../../../modules/nf-core/rseqc/inferexperiment/main.nf' +include { RSEQC_INFEREXPERIMENT } from '../../../../../modules/nf-core/rseqc/inferexperiment/main.nf' workflow test_rseqc_inferexperiment { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/rseqc/innerdistance/main.nf b/tests/modules/nf-core/rseqc/innerdistance/main.nf index b44db9e49a7..48130d493e9 100644 --- a/tests/modules/nf-core/rseqc/innerdistance/main.nf +++ b/tests/modules/nf-core/rseqc/innerdistance/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_INNERDISTANCE } from '../../../../modules/nf-core/rseqc/innerdistance/main.nf' +include { RSEQC_INNERDISTANCE } from '../../../../../modules/nf-core/rseqc/innerdistance/main.nf' workflow test_rseqc_innerdistance { input = [ [ id:'test', single_end: false ], // meta map diff --git a/tests/modules/nf-core/rseqc/junctionannotation/main.nf b/tests/modules/nf-core/rseqc/junctionannotation/main.nf index 1dc7983063f..90fbbc9660b 100644 --- a/tests/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/tests/modules/nf-core/rseqc/junctionannotation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_JUNCTIONANNOTATION } from '../../../../modules/nf-core/rseqc/junctionannotation/main.nf' +include { RSEQC_JUNCTIONANNOTATION } from '../../../../../modules/nf-core/rseqc/junctionannotation/main.nf' workflow test_rseqc_junctionannotation { input = [ diff --git a/tests/modules/nf-core/rseqc/junctionsaturation/main.nf b/tests/modules/nf-core/rseqc/junctionsaturation/main.nf index dd3a8fa1706..bcb8981c085 100644 --- a/tests/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/tests/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_JUNCTIONSATURATION } from '../../../../modules/nf-core/rseqc/junctionsaturation/main.nf' +include { RSEQC_JUNCTIONSATURATION } from '../../../../../modules/nf-core/rseqc/junctionsaturation/main.nf' workflow test_rseqc_junctionsaturation { input = [ diff --git a/tests/modules/nf-core/rseqc/readdistribution/main.nf b/tests/modules/nf-core/rseqc/readdistribution/main.nf index 130a2ac1d5b..5bcbe38324d 100644 --- a/tests/modules/nf-core/rseqc/readdistribution/main.nf +++ b/tests/modules/nf-core/rseqc/readdistribution/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_READDISTRIBUTION } from '../../../../modules/nf-core/rseqc/readdistribution/main.nf' +include { RSEQC_READDISTRIBUTION } from '../../../../../modules/nf-core/rseqc/readdistribution/main.nf' workflow test_rseqc_readdistribution { input = [ [ id:'test', single_end: false ], // meta map diff --git a/tests/modules/nf-core/rseqc/readduplication/main.nf b/tests/modules/nf-core/rseqc/readduplication/main.nf index 07236b53626..f641d265a0d 100644 --- a/tests/modules/nf-core/rseqc/readduplication/main.nf +++ b/tests/modules/nf-core/rseqc/readduplication/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_READDUPLICATION } from '../../../../modules/nf-core/rseqc/readduplication/main.nf' +include { RSEQC_READDUPLICATION } from '../../../../../modules/nf-core/rseqc/readduplication/main.nf' workflow test_rseqc_readduplication { input = [ [ id:'test', single_end: false ], // meta map diff --git a/tests/modules/nf-core/rseqc/tin/main.nf b/tests/modules/nf-core/rseqc/tin/main.nf index adb294cfcdb..a91fb3e2302 100644 --- a/tests/modules/nf-core/rseqc/tin/main.nf +++ b/tests/modules/nf-core/rseqc/tin/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RSEQC_TIN } from '../../../../modules/nf-core/rseqc/tin/main.nf' +include { RSEQC_TIN } from '../../../../../modules/nf-core/rseqc/tin/main.nf' workflow test_rseqc_tin { diff --git a/tests/modules/nf-core/rtgtools/pedfilter/main.nf b/tests/modules/nf-core/rtgtools/pedfilter/main.nf index f667e8f55d9..97421523e1f 100644 --- a/tests/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/tests/modules/nf-core/rtgtools/pedfilter/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { RTGTOOLS_PEDFILTER } from '../../../../modules/nf-core/rtgtools/pedfilter/main.nf' +include { RTGTOOLS_PEDFILTER } from '../../../../../modules/nf-core/rtgtools/pedfilter/main.nf' workflow test_rtgtools_pedfilter { diff --git a/tests/modules/nf-core/rtgtools/vcfeval/main.nf b/tests/modules/nf-core/rtgtools/vcfeval/main.nf index 8c65581bcd9..df6a9850b95 100644 --- a/tests/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/tests/modules/nf-core/rtgtools/vcfeval/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { RTGTOOLS_VCFEVAL } from '../../../../modules/nf-core/rtgtools/vcfeval/main.nf' -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { RTGTOOLS_VCFEVAL } from '../../../../../modules/nf-core/rtgtools/vcfeval/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_rtgtools_vcfeval { diff --git a/tests/modules/nf-core/salmon/index/main.nf b/tests/modules/nf-core/salmon/index/main.nf index 55525b4eeee..4ebb83688cd 100644 --- a/tests/modules/nf-core/salmon/index/main.nf +++ b/tests/modules/nf-core/salmon/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../../modules/nf-core/salmon/index/main.nf' +include { SALMON_INDEX } from '../../../../../modules/nf-core/salmon/index/main.nf' workflow test_salmon_index { genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/salmon/quant/main.nf b/tests/modules/nf-core/salmon/quant/main.nf index 8cf2b1b00e3..5f402193db5 100644 --- a/tests/modules/nf-core/salmon/quant/main.nf +++ b/tests/modules/nf-core/salmon/quant/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SALMON_INDEX } from '../../../../modules/nf-core/salmon/index/main.nf' -include { SALMON_QUANT } from '../../../../modules/nf-core/salmon/quant/main.nf' +include { SALMON_INDEX } from '../../../../../modules/nf-core/salmon/index/main.nf' +include { SALMON_QUANT } from '../../../../../modules/nf-core/salmon/quant/main.nf' workflow test_salmon_quant_single_end { diff --git a/tests/modules/nf-core/samblaster/main.nf b/tests/modules/nf-core/samblaster/main.nf index 17e769f5419..2e54aefe862 100644 --- a/tests/modules/nf-core/samblaster/main.nf +++ b/tests/modules/nf-core/samblaster/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMBLASTER } from '../../../modules/nf-core/samblaster/main.nf' +include { SAMBLASTER } from '../../../../modules/nf-core/samblaster/main.nf' workflow test_samblaster { diff --git a/tests/modules/nf-core/samtools/ampliconclip/main.nf b/tests/modules/nf-core/samtools/ampliconclip/main.nf index 2b2646bc3ca..9f571ad6f1c 100644 --- a/tests/modules/nf-core/samtools/ampliconclip/main.nf +++ b/tests/modules/nf-core/samtools/ampliconclip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/nf-core/samtools/ampliconclip/main.nf' +include { SAMTOOLS_AMPLICONCLIP } from '../../../../../modules/nf-core/samtools/ampliconclip/main.nf' workflow test_samtools_ampliconclip_no_stats_no_rejects { diff --git a/tests/modules/nf-core/samtools/bam2fq/main.nf b/tests/modules/nf-core/samtools/bam2fq/main.nf index 70c8fe864bf..847e6cf6723 100644 --- a/tests/modules/nf-core/samtools/bam2fq/main.nf +++ b/tests/modules/nf-core/samtools/bam2fq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_BAM2FQ } from '../../../../modules/nf-core/samtools/bam2fq/main.nf' +include { SAMTOOLS_BAM2FQ } from '../../../../../modules/nf-core/samtools/bam2fq/main.nf' workflow test_samtools_bam2fq_nosplit { diff --git a/tests/modules/nf-core/samtools/collate/main.nf b/tests/modules/nf-core/samtools/collate/main.nf index 34b62eef42e..9e3e8805c71 100644 --- a/tests/modules/nf-core/samtools/collate/main.nf +++ b/tests/modules/nf-core/samtools/collate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COLLATE } from '../../../../modules/nf-core/samtools/collate/main.nf' +include { SAMTOOLS_COLLATE } from '../../../../../modules/nf-core/samtools/collate/main.nf' workflow test_samtools_collate { diff --git a/tests/modules/nf-core/samtools/collatefastq/main.nf b/tests/modules/nf-core/samtools/collatefastq/main.nf index 2c629750351..57c732a6ff2 100644 --- a/tests/modules/nf-core/samtools/collatefastq/main.nf +++ b/tests/modules/nf-core/samtools/collatefastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COLLATEFASTQ } from '../../../../modules/nf-core/samtools/collatefastq/main.nf' +include { SAMTOOLS_COLLATEFASTQ } from '../../../../../modules/nf-core/samtools/collatefastq/main.nf' workflow test_samtools_collatefastq { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/convert/main.nf b/tests/modules/nf-core/samtools/convert/main.nf index cdde49aa94a..38b00b96d05 100644 --- a/tests/modules/nf-core/samtools/convert/main.nf +++ b/tests/modules/nf-core/samtools/convert/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/nf-core/samtools/convert/main.nf' -include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/nf-core/samtools/convert/main.nf' +include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../../modules/nf-core/samtools/convert/main.nf' +include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../../modules/nf-core/samtools/convert/main.nf' workflow test_samtools_convert_bamtocram { diff --git a/tests/modules/nf-core/samtools/depth/main.nf b/tests/modules/nf-core/samtools/depth/main.nf index 4d88ac588ce..23dae538463 100644 --- a/tests/modules/nf-core/samtools/depth/main.nf +++ b/tests/modules/nf-core/samtools/depth/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_DEPTH } from '../../../../modules/nf-core/samtools/depth/main.nf' +include { SAMTOOLS_DEPTH } from '../../../../../modules/nf-core/samtools/depth/main.nf' workflow test_samtools_depth { diff --git a/tests/modules/nf-core/samtools/dict/main.nf b/tests/modules/nf-core/samtools/dict/main.nf index b05fde55c57..7bac114a4f1 100644 --- a/tests/modules/nf-core/samtools/dict/main.nf +++ b/tests/modules/nf-core/samtools/dict/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_DICT } from '../../../../modules/nf-core/samtools/dict/main.nf' +include { SAMTOOLS_DICT } from '../../../../../modules/nf-core/samtools/dict/main.nf' workflow test_samtools_dict { diff --git a/tests/modules/nf-core/samtools/faidx/main.nf b/tests/modules/nf-core/samtools/faidx/main.nf index 0f55475c025..e07229915db 100644 --- a/tests/modules/nf-core/samtools/faidx/main.nf +++ b/tests/modules/nf-core/samtools/faidx/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FAIDX } from '../../../../modules/nf-core/samtools/faidx/main.nf' +include { SAMTOOLS_FAIDX } from '../../../../../modules/nf-core/samtools/faidx/main.nf' workflow test_samtools_faidx { diff --git a/tests/modules/nf-core/samtools/fasta/main.nf b/tests/modules/nf-core/samtools/fasta/main.nf index 83b68728653..f477209bcf1 100644 --- a/tests/modules/nf-core/samtools/fasta/main.nf +++ b/tests/modules/nf-core/samtools/fasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FASTA } from '../../../../modules/nf-core/samtools/fasta/main.nf' +include { SAMTOOLS_FASTA } from '../../../../../modules/nf-core/samtools/fasta/main.nf' workflow test_samtools_fasta { diff --git a/tests/modules/nf-core/samtools/fastq/main.nf b/tests/modules/nf-core/samtools/fastq/main.nf index aa454e811a0..b7997101d63 100644 --- a/tests/modules/nf-core/samtools/fastq/main.nf +++ b/tests/modules/nf-core/samtools/fastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FASTQ } from '../../../../modules/nf-core/samtools/fastq/main.nf' +include { SAMTOOLS_FASTQ } from '../../../../../modules/nf-core/samtools/fastq/main.nf' workflow test_samtools_fastq { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/fixmate/main.nf b/tests/modules/nf-core/samtools/fixmate/main.nf index 8da5be726b6..e2a1725f5a4 100644 --- a/tests/modules/nf-core/samtools/fixmate/main.nf +++ b/tests/modules/nf-core/samtools/fixmate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FIXMATE } from '../../../../modules/nf-core/samtools/fixmate/main.nf' +include { SAMTOOLS_FIXMATE } from '../../../../../modules/nf-core/samtools/fixmate/main.nf' workflow test_samtools_fixmate { diff --git a/tests/modules/nf-core/samtools/flagstat/main.nf b/tests/modules/nf-core/samtools/flagstat/main.nf index bb30f518be4..c1a435f02a7 100644 --- a/tests/modules/nf-core/samtools/flagstat/main.nf +++ b/tests/modules/nf-core/samtools/flagstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FLAGSTAT } from '../../../../modules/nf-core/samtools/flagstat/main.nf' +include { SAMTOOLS_FLAGSTAT } from '../../../../../modules/nf-core/samtools/flagstat/main.nf' workflow test_samtools_flagstat { input = [ diff --git a/tests/modules/nf-core/samtools/getrg/main.nf b/tests/modules/nf-core/samtools/getrg/main.nf index 3ce9f80c9c2..19403d2f124 100644 --- a/tests/modules/nf-core/samtools/getrg/main.nf +++ b/tests/modules/nf-core/samtools/getrg/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_GETRG } from '../../../../modules/nf-core/samtools/getrg/main.nf' +include { SAMTOOLS_GETRG } from '../../../../../modules/nf-core/samtools/getrg/main.nf' workflow test_samtools_getrg { diff --git a/tests/modules/nf-core/samtools/idxstats/main.nf b/tests/modules/nf-core/samtools/idxstats/main.nf index 83b0607e30a..4a29252eb3b 100644 --- a/tests/modules/nf-core/samtools/idxstats/main.nf +++ b/tests/modules/nf-core/samtools/idxstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_IDXSTATS } from '../../../../modules/nf-core/samtools/idxstats/main.nf' +include { SAMTOOLS_IDXSTATS } from '../../../../../modules/nf-core/samtools/idxstats/main.nf' workflow test_samtools_idxstats { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/index/main.nf b/tests/modules/nf-core/samtools/index/main.nf index ff952b5a36b..880f44f3308 100644 --- a/tests/modules/nf-core/samtools/index/main.nf +++ b/tests/modules/nf-core/samtools/index/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/nf-core/samtools/index/main.nf' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/nf-core/samtools/index/main.nf' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/nf-core/samtools/index/main.nf' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../../modules/nf-core/samtools/index/main.nf' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../../modules/nf-core/samtools/index/main.nf' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../../modules/nf-core/samtools/index/main.nf' workflow test_samtools_index_bai { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/markdup/main.nf b/tests/modules/nf-core/samtools/markdup/main.nf index f96bfc55442..6d8cb99394b 100644 --- a/tests/modules/nf-core/samtools/markdup/main.nf +++ b/tests/modules/nf-core/samtools/markdup/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COLLATE } from '../../../../modules/nf-core/samtools/collate/main.nf' -include { SAMTOOLS_FIXMATE } from '../../../../modules/nf-core/samtools/fixmate/main.nf' -include { SAMTOOLS_SORT } from '../../../../modules/nf-core/samtools/sort/main.nf' -include { SAMTOOLS_MARKDUP } from '../../../../modules/nf-core/samtools/markdup/main.nf' +include { SAMTOOLS_COLLATE } from '../../../../../modules/nf-core/samtools/collate/main.nf' +include { SAMTOOLS_FIXMATE } from '../../../../../modules/nf-core/samtools/fixmate/main.nf' +include { SAMTOOLS_SORT } from '../../../../../modules/nf-core/samtools/sort/main.nf' +include { SAMTOOLS_MARKDUP } from '../../../../../modules/nf-core/samtools/markdup/main.nf' workflow test_samtools_markdup { diff --git a/tests/modules/nf-core/samtools/merge/main.nf b/tests/modules/nf-core/samtools/merge/main.nf index 3e41ffc7769..34d96d1ec7c 100644 --- a/tests/modules/nf-core/samtools/merge/main.nf +++ b/tests/modules/nf-core/samtools/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_MERGE } from '../../../../modules/nf-core/samtools/merge/main.nf' +include { SAMTOOLS_MERGE } from '../../../../../modules/nf-core/samtools/merge/main.nf' workflow test_samtools_merge { input = [ [ id: 'test' ], // meta map diff --git a/tests/modules/nf-core/samtools/mpileup/main.nf b/tests/modules/nf-core/samtools/mpileup/main.nf index 4ee131c29bf..ce8540a06c2 100644 --- a/tests/modules/nf-core/samtools/mpileup/main.nf +++ b/tests/modules/nf-core/samtools/mpileup/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_MPILEUP } from '../../../../modules/nf-core/samtools/mpileup/main.nf' +include { SAMTOOLS_MPILEUP } from '../../../../../modules/nf-core/samtools/mpileup/main.nf' workflow test_samtools_mpileup { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/sort/main.nf b/tests/modules/nf-core/samtools/sort/main.nf index 5b9d6890a46..8811c00e4ae 100644 --- a/tests/modules/nf-core/samtools/sort/main.nf +++ b/tests/modules/nf-core/samtools/sort/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_SORT } from '../../../../modules/nf-core/samtools/sort/main.nf' +include { SAMTOOLS_SORT } from '../../../../../modules/nf-core/samtools/sort/main.nf' workflow test_samtools_sort { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/stats/main.nf b/tests/modules/nf-core/samtools/stats/main.nf index 596ba1fcae8..523056ae72c 100644 --- a/tests/modules/nf-core/samtools/stats/main.nf +++ b/tests/modules/nf-core/samtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_STATS } from '../../../../modules/nf-core/samtools/stats/main.nf' +include { SAMTOOLS_STATS } from '../../../../../modules/nf-core/samtools/stats/main.nf' workflow test_samtools_stats { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/samtools/view/main.nf b/tests/modules/nf-core/samtools/view/main.nf index 210a493adf1..f30eeefe88c 100644 --- a/tests/modules/nf-core/samtools/view/main.nf +++ b/tests/modules/nf-core/samtools/view/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_VIEW } from '../../../../modules/nf-core/samtools/view/main.nf' +include { SAMTOOLS_VIEW } from '../../../../../modules/nf-core/samtools/view/main.nf' workflow test_samtools_view { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/scoary/main.nf b/tests/modules/nf-core/scoary/main.nf index 59006b049e7..6d606eabcf6 100644 --- a/tests/modules/nf-core/scoary/main.nf +++ b/tests/modules/nf-core/scoary/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SCOARY } from '../../../modules/nf-core/scoary/main.nf' +include { SCOARY } from '../../../../modules/nf-core/scoary/main.nf' workflow test_scoary { diff --git a/tests/modules/nf-core/scramble/clusteranalysis/main.nf b/tests/modules/nf-core/scramble/clusteranalysis/main.nf index d9444c955d9..58020321afb 100644 --- a/tests/modules/nf-core/scramble/clusteranalysis/main.nf +++ b/tests/modules/nf-core/scramble/clusteranalysis/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SCRAMBLE_CLUSTERANALYSIS } from '../../../../modules/nf-core/scramble/clusteranalysis/main.nf' -include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/nf-core/scramble/clusteridentifier/main.nf' +include { SCRAMBLE_CLUSTERANALYSIS } from '../../../../../modules/nf-core/scramble/clusteranalysis/main.nf' +include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../../modules/nf-core/scramble/clusteridentifier/main.nf' workflow test_scramble_clusteranalysis { diff --git a/tests/modules/nf-core/scramble/clusteridentifier/main.nf b/tests/modules/nf-core/scramble/clusteridentifier/main.nf index 1884a701881..2c2602652cd 100644 --- a/tests/modules/nf-core/scramble/clusteridentifier/main.nf +++ b/tests/modules/nf-core/scramble/clusteridentifier/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../modules/nf-core/scramble/clusteridentifier/main.nf' +include { SCRAMBLE_CLUSTERIDENTIFIER } from '../../../../../modules/nf-core/scramble/clusteridentifier/main.nf' workflow test_scramble_clusteridentifier_bam { diff --git a/tests/modules/nf-core/seacr/callpeak/main.nf b/tests/modules/nf-core/seacr/callpeak/main.nf index 789e4f179bb..002115c81b0 100644 --- a/tests/modules/nf-core/seacr/callpeak/main.nf +++ b/tests/modules/nf-core/seacr/callpeak/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEACR_CALLPEAK } from '../../../../modules/nf-core/seacr/callpeak/main.nf' +include { SEACR_CALLPEAK } from '../../../../../modules/nf-core/seacr/callpeak/main.nf' workflow test_seacr_callpeak { input = [ [ id:'test_1'], diff --git a/tests/modules/nf-core/seqkit/pair/main.nf b/tests/modules/nf-core/seqkit/pair/main.nf index b8b9070743d..f8f57e37b1a 100644 --- a/tests/modules/nf-core/seqkit/pair/main.nf +++ b/tests/modules/nf-core/seqkit/pair/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQKIT_PAIR } from '../../../../modules/nf-core/seqkit/pair/main.nf' +include { SEQKIT_PAIR } from '../../../../../modules/nf-core/seqkit/pair/main.nf' workflow test_seqkit_pair { diff --git a/tests/modules/nf-core/seqkit/replace/main.nf b/tests/modules/nf-core/seqkit/replace/main.nf index 8cc2ce9ad9a..a066a33f10c 100644 --- a/tests/modules/nf-core/seqkit/replace/main.nf +++ b/tests/modules/nf-core/seqkit/replace/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SEQKIT_REPLACE } from '../../../../modules/nf-core/seqkit/replace/main.nf' -include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../modules/nf-core/seqkit/replace/main.nf' +include { SEQKIT_REPLACE } from '../../../../../modules/nf-core/seqkit/replace/main.nf' +include { SEQKIT_REPLACE as SEQKIT_REPLACEUNCOMP } from '../../../../../modules/nf-core/seqkit/replace/main.nf' workflow test_seqkit_replace { diff --git a/tests/modules/nf-core/seqkit/split2/main.nf b/tests/modules/nf-core/seqkit/split2/main.nf index 248e9f915cb..39d6a76051c 100644 --- a/tests/modules/nf-core/seqkit/split2/main.nf +++ b/tests/modules/nf-core/seqkit/split2/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../modules/nf-core/seqkit/split2/main.nf' -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../modules/nf-core/seqkit/split2/main.nf' -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../modules/nf-core/seqkit/split2/main.nf' +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../../modules/nf-core/seqkit/split2/main.nf' +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../../modules/nf-core/seqkit/split2/main.nf' +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../../modules/nf-core/seqkit/split2/main.nf' workflow test_seqkit_split2_single_end_length { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/seqkit/stats/main.nf b/tests/modules/nf-core/seqkit/stats/main.nf index e516c834805..5d6fc6eb2d4 100644 --- a/tests/modules/nf-core/seqkit/stats/main.nf +++ b/tests/modules/nf-core/seqkit/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQKIT_STATS } from '../../../../modules/nf-core/seqkit/stats/main.nf' +include { SEQKIT_STATS } from '../../../../../modules/nf-core/seqkit/stats/main.nf' workflow test_seqkit_stats_single_end { diff --git a/tests/modules/nf-core/seqsero2/main.nf b/tests/modules/nf-core/seqsero2/main.nf index b3ee1261bb7..40908120995 100644 --- a/tests/modules/nf-core/seqsero2/main.nf +++ b/tests/modules/nf-core/seqsero2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQSERO2 } from '../../../modules/nf-core/seqsero2/main.nf' +include { SEQSERO2 } from '../../../../modules/nf-core/seqsero2/main.nf' workflow test_seqsero2 { diff --git a/tests/modules/nf-core/seqtk/mergepe/main.nf b/tests/modules/nf-core/seqtk/mergepe/main.nf index 9c980d5d976..af82e367131 100644 --- a/tests/modules/nf-core/seqtk/mergepe/main.nf +++ b/tests/modules/nf-core/seqtk/mergepe/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_MERGEPE } from '../../../../modules/nf-core/seqtk/mergepe/main.nf' +include { SEQTK_MERGEPE } from '../../../../../modules/nf-core/seqtk/mergepe/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/seqtk/rename/main.nf b/tests/modules/nf-core/seqtk/rename/main.nf index ea48a880a33..eb225d3e759 100644 --- a/tests/modules/nf-core/seqtk/rename/main.nf +++ b/tests/modules/nf-core/seqtk/rename/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_RENAME } from '../../../../modules/nf-core/seqtk/rename/main.nf' +include { SEQTK_RENAME } from '../../../../../modules/nf-core/seqtk/rename/main.nf' workflow test_seqtk_rename { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seqtk/sample/main.nf b/tests/modules/nf-core/seqtk/sample/main.nf index e380a052b77..5e0d30e1702 100644 --- a/tests/modules/nf-core/seqtk/sample/main.nf +++ b/tests/modules/nf-core/seqtk/sample/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_SAMPLE } from '../../../../modules/nf-core/seqtk/sample/main.nf' +include { SEQTK_SAMPLE } from '../../../../../modules/nf-core/seqtk/sample/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/seqtk/seq/main.nf b/tests/modules/nf-core/seqtk/seq/main.nf index a30e1d3f1ac..4feff0d7e3e 100644 --- a/tests/modules/nf-core/seqtk/seq/main.nf +++ b/tests/modules/nf-core/seqtk/seq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_SEQ } from '../../../../modules/nf-core/seqtk/seq/main.nf' +include { SEQTK_SEQ } from '../../../../../modules/nf-core/seqtk/seq/main.nf' workflow test_seqtk_seq { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seqtk/subseq/main.nf b/tests/modules/nf-core/seqtk/subseq/main.nf index 28ad03af951..f96fa9f8a4d 100644 --- a/tests/modules/nf-core/seqtk/subseq/main.nf +++ b/tests/modules/nf-core/seqtk/subseq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQTK_SUBSEQ } from '../../../../modules/nf-core/seqtk/subseq/main.nf' +include { SEQTK_SUBSEQ } from '../../../../../modules/nf-core/seqtk/subseq/main.nf' workflow test_seqtk_subseq { diff --git a/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf b/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf index 9da93c79af8..9304d805314 100755 --- a/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/tests/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/nf-core/sequenzautils/bam2seqz/main.nf' +include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../../modules/nf-core/sequenzautils/bam2seqz/main.nf' workflow test_sequenzautils_bam2seqz { diff --git a/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf b/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf index 9e7da379e20..776e4f17f32 100644 --- a/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf +++ b/tests/modules/nf-core/sequenzautils/gcwiggle/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQUENZAUTILS_GCWIGGLE } from '../../../../modules/nf-core/sequenzautils/gcwiggle/main.nf' +include { SEQUENZAUTILS_GCWIGGLE } from '../../../../../modules/nf-core/sequenzautils/gcwiggle/main.nf' workflow test_sequenzautils_gcwiggle { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seqwish/induce/main.nf b/tests/modules/nf-core/seqwish/induce/main.nf index c7e79c66198..20aae22b07e 100644 --- a/tests/modules/nf-core/seqwish/induce/main.nf +++ b/tests/modules/nf-core/seqwish/induce/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEQWISH_INDUCE } from '../../../../modules/nf-core/seqwish/induce/main.nf' +include { SEQWISH_INDUCE } from '../../../../../modules/nf-core/seqwish/induce/main.nf' workflow test_seqwish_induce_transcriptome { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/seroba/run/main.nf b/tests/modules/nf-core/seroba/run/main.nf index d848ddaa1b6..0f58c610d2c 100644 --- a/tests/modules/nf-core/seroba/run/main.nf +++ b/tests/modules/nf-core/seroba/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SEROBA_RUN } from '../../../../modules/nf-core/seroba/run/main.nf' +include { SEROBA_RUN } from '../../../../../modules/nf-core/seroba/run/main.nf' workflow test_seroba_run { diff --git a/tests/modules/nf-core/sexdeterrmine/main.nf b/tests/modules/nf-core/sexdeterrmine/main.nf index 6ad76a6e7fb..10d3e53f469 100644 --- a/tests/modules/nf-core/sexdeterrmine/main.nf +++ b/tests/modules/nf-core/sexdeterrmine/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_DEPTH } from '../../../modules/nf-core/samtools/depth/main.nf' -include { SEXDETERRMINE } from '../../../modules/nf-core/sexdeterrmine/main.nf' +include { SAMTOOLS_DEPTH } from '../../../../modules/nf-core/samtools/depth/main.nf' +include { SEXDETERRMINE } from '../../../../modules/nf-core/sexdeterrmine/main.nf' workflow test_sexdeterrmine { diff --git a/tests/modules/nf-core/shasta/main.nf b/tests/modules/nf-core/shasta/main.nf index 68bbce3d4b9..0bf5298a365 100644 --- a/tests/modules/nf-core/shasta/main.nf +++ b/tests/modules/nf-core/shasta/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SHASTA } from '../../../modules/nf-core/shasta/main.nf' +include { SHASTA } from '../../../../modules/nf-core/shasta/main.nf' workflow test_shasta { diff --git a/tests/modules/nf-core/shasum/main.nf b/tests/modules/nf-core/shasum/main.nf index d3457d8c115..d7f3ce50680 100644 --- a/tests/modules/nf-core/shasum/main.nf +++ b/tests/modules/nf-core/shasum/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SHASUM } from '../../../modules/nf-core/shasum/main.nf' +include { SHASUM } from '../../../../modules/nf-core/shasum/main.nf' workflow test_shasum { diff --git a/tests/modules/nf-core/shigatyper/main.nf b/tests/modules/nf-core/shigatyper/main.nf index a234df007f2..e04fd5ad2f7 100644 --- a/tests/modules/nf-core/shigatyper/main.nf +++ b/tests/modules/nf-core/shigatyper/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SHIGATYPER } from '../../../modules/nf-core/shigatyper/main.nf' +include { SHIGATYPER } from '../../../../modules/nf-core/shigatyper/main.nf' workflow test_shigatyper_pe { diff --git a/tests/modules/nf-core/shovill/main.nf b/tests/modules/nf-core/shovill/main.nf index 6c48df62b35..5596c7cb78a 100644 --- a/tests/modules/nf-core/shovill/main.nf +++ b/tests/modules/nf-core/shovill/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { SHOVILL } from '../../../modules/nf-core/shovill/main.nf' -include { SHOVILL as SHOVILL_SKESA } from '../../../modules/nf-core/shovill/main.nf' -include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/nf-core/shovill/main.nf' -include { SHOVILL as SHOVILL_VELVET } from '../../../modules/nf-core/shovill/main.nf' +include { SHOVILL } from '../../../../modules/nf-core/shovill/main.nf' +include { SHOVILL as SHOVILL_SKESA } from '../../../../modules/nf-core/shovill/main.nf' +include { SHOVILL as SHOVILL_MEGAHIT } from '../../../../modules/nf-core/shovill/main.nf' +include { SHOVILL as SHOVILL_VELVET } from '../../../../modules/nf-core/shovill/main.nf' workflow test_shovill { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/sistr/main.nf b/tests/modules/nf-core/sistr/main.nf index c25fe807855..4b8948d23f3 100644 --- a/tests/modules/nf-core/sistr/main.nf +++ b/tests/modules/nf-core/sistr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SISTR } from '../../../modules/nf-core/sistr/main.nf' +include { SISTR } from '../../../../modules/nf-core/sistr/main.nf' workflow test_sistr { diff --git a/tests/modules/nf-core/slimfastq/main.nf b/tests/modules/nf-core/slimfastq/main.nf index a0ea9ab3e70..2993eb981f9 100644 --- a/tests/modules/nf-core/slimfastq/main.nf +++ b/tests/modules/nf-core/slimfastq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SLIMFASTQ } from '../../../modules/nf-core/slimfastq/main.nf' +include { SLIMFASTQ } from '../../../../modules/nf-core/slimfastq/main.nf' workflow test_slimfastq_single_end { diff --git a/tests/modules/nf-core/snapaligner/align/main.nf b/tests/modules/nf-core/snapaligner/align/main.nf index b91302f32b3..8f30888369d 100644 --- a/tests/modules/nf-core/snapaligner/align/main.nf +++ b/tests/modules/nf-core/snapaligner/align/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SNAPALIGNER_INDEX } from '../../../../modules/nf-core/snapaligner/index/main.nf' -include { SNAPALIGNER_ALIGN } from '../../../../modules/nf-core/snapaligner/align/main.nf' +include { SNAPALIGNER_INDEX } from '../../../../../modules/nf-core/snapaligner/index/main.nf' +include { SNAPALIGNER_ALIGN } from '../../../../../modules/nf-core/snapaligner/align/main.nf' workflow test_snapaligner_single { diff --git a/tests/modules/nf-core/snapaligner/index/main.nf b/tests/modules/nf-core/snapaligner/index/main.nf index f43c40b3371..a1b01c36f9c 100644 --- a/tests/modules/nf-core/snapaligner/index/main.nf +++ b/tests/modules/nf-core/snapaligner/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNAPALIGNER_INDEX } from '../../../../modules/nf-core/snapaligner/index/main.nf' +include { SNAPALIGNER_INDEX } from '../../../../../modules/nf-core/snapaligner/index/main.nf' workflow test_snapaligner_index { SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[]) diff --git a/tests/modules/nf-core/snippy/core/main.nf b/tests/modules/nf-core/snippy/core/main.nf index 26949c8a575..3f786c371f4 100644 --- a/tests/modules/nf-core/snippy/core/main.nf +++ b/tests/modules/nf-core/snippy/core/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SNIPPY_RUN } from '../../../../modules/nf-core/snippy/run/main.nf' -include { SNIPPY_CORE } from '../../../../modules/nf-core/snippy/core/main.nf' +include { SNIPPY_RUN } from '../../../../../modules/nf-core/snippy/run/main.nf' +include { SNIPPY_CORE } from '../../../../../modules/nf-core/snippy/core/main.nf' workflow test_snippy_core { diff --git a/tests/modules/nf-core/snippy/run/main.nf b/tests/modules/nf-core/snippy/run/main.nf index 142fd091284..1150c893701 100644 --- a/tests/modules/nf-core/snippy/run/main.nf +++ b/tests/modules/nf-core/snippy/run/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNIPPY_RUN } from '../../../../modules/nf-core/snippy/run/main.nf' +include { SNIPPY_RUN } from '../../../../../modules/nf-core/snippy/run/main.nf' workflow test_snippy_run { diff --git a/tests/modules/nf-core/snpdists/main.nf b/tests/modules/nf-core/snpdists/main.nf index 625b3ddd3cb..3cbf0e12cd0 100644 --- a/tests/modules/nf-core/snpdists/main.nf +++ b/tests/modules/nf-core/snpdists/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPDISTS } from '../../../modules/nf-core/snpdists/main.nf' +include { SNPDISTS } from '../../../../modules/nf-core/snpdists/main.nf' workflow test_snpdists { diff --git a/tests/modules/nf-core/snpeff/main.nf b/tests/modules/nf-core/snpeff/main.nf index 23b3cdbcc97..1670076a249 100644 --- a/tests/modules/nf-core/snpeff/main.nf +++ b/tests/modules/nf-core/snpeff/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPEFF } from '../../../modules/nf-core/snpeff/main.nf' +include { SNPEFF } from '../../../../modules/nf-core/snpeff/main.nf' workflow test_snpeff { input = [ diff --git a/tests/modules/nf-core/snpsift/split/main.nf b/tests/modules/nf-core/snpsift/split/main.nf index 2431840a4c8..11cee60d860 100644 --- a/tests/modules/nf-core/snpsift/split/main.nf +++ b/tests/modules/nf-core/snpsift/split/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPSIFT_SPLIT } from '../../../../modules/nf-core/snpsift/split/main.nf' +include { SNPSIFT_SPLIT } from '../../../../../modules/nf-core/snpsift/split/main.nf' workflow test_snpsift_split_base { diff --git a/tests/modules/nf-core/snpsites/main.nf b/tests/modules/nf-core/snpsites/main.nf index 25e0051d500..a6a43095212 100644 --- a/tests/modules/nf-core/snpsites/main.nf +++ b/tests/modules/nf-core/snpsites/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SNPSITES } from '../../../modules/nf-core/snpsites/main.nf' +include { SNPSITES } from '../../../../modules/nf-core/snpsites/main.nf' workflow test_snpsites { diff --git a/tests/modules/nf-core/somalier/extract/main.nf b/tests/modules/nf-core/somalier/extract/main.nf index cc47c1f4ff6..68847626e83 100644 --- a/tests/modules/nf-core/somalier/extract/main.nf +++ b/tests/modules/nf-core/somalier/extract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SOMALIER_EXTRACT } from '../../../../modules/nf-core/somalier/extract/main.nf' +include { SOMALIER_EXTRACT } from '../../../../../modules/nf-core/somalier/extract/main.nf' fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/somalier/relate/main.nf b/tests/modules/nf-core/somalier/relate/main.nf index 2387fe6837b..14b1977e635 100644 --- a/tests/modules/nf-core/somalier/relate/main.nf +++ b/tests/modules/nf-core/somalier/relate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SOMALIER_RELATE } from '../../../../modules/nf-core/somalier/relate/main.nf' +include { SOMALIER_RELATE } from '../../../../../modules/nf-core/somalier/relate/main.nf' workflow test_somalier_relate { diff --git a/tests/modules/nf-core/sourmash/sketch/main.nf b/tests/modules/nf-core/sourmash/sketch/main.nf index 49fd0ce1df9..bb398d9a893 100644 --- a/tests/modules/nf-core/sourmash/sketch/main.nf +++ b/tests/modules/nf-core/sourmash/sketch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SOURMASH_SKETCH } from '../../../../modules/nf-core/sourmash/sketch/main.nf' +include { SOURMASH_SKETCH } from '../../../../../modules/nf-core/sourmash/sketch/main.nf' workflow test_sourmash_sketch { diff --git a/tests/modules/nf-core/spades/main.nf b/tests/modules/nf-core/spades/main.nf index 58b07bc9647..9305112956a 100644 --- a/tests/modules/nf-core/spades/main.nf +++ b/tests/modules/nf-core/spades/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SPADES } from '../../../modules/nf-core/spades/main.nf' +include { SPADES } from '../../../../modules/nf-core/spades/main.nf' workflow test_spades_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/spatyper/main.nf b/tests/modules/nf-core/spatyper/main.nf index 62a7e0c5ebe..5f6ced1d393 100644 --- a/tests/modules/nf-core/spatyper/main.nf +++ b/tests/modules/nf-core/spatyper/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SPATYPER } from '../../../modules/nf-core/spatyper/main.nf' -include { SPATYPER as SPATYPER_ENRICH } from '../../../modules/nf-core/spatyper/main.nf' +include { SPATYPER } from '../../../../modules/nf-core/spatyper/main.nf' +include { SPATYPER as SPATYPER_ENRICH } from '../../../../modules/nf-core/spatyper/main.nf' workflow test_spatyper { input = [ [ id:'test' ], diff --git a/tests/modules/nf-core/sratools/fasterqdump/main.nf b/tests/modules/nf-core/sratools/fasterqdump/main.nf index 57984ccb1b8..922387069a0 100644 --- a/tests/modules/nf-core/sratools/fasterqdump/main.nf +++ b/tests/modules/nf-core/sratools/fasterqdump/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' -include { SRATOOLS_FASTERQDUMP } from '../../../../modules/nf-core/sratools/fasterqdump/main.nf' +include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' +include { SRATOOLS_FASTERQDUMP } from '../../../../../modules/nf-core/sratools/fasterqdump/main.nf' workflow test_sratools_fasterqdump_single_end { diff --git a/tests/modules/nf-core/sratools/prefetch/main.nf b/tests/modules/nf-core/sratools/prefetch/main.nf index cd59e61567b..be20bbc1bce 100644 --- a/tests/modules/nf-core/sratools/prefetch/main.nf +++ b/tests/modules/nf-core/sratools/prefetch/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SRATOOLS_PREFETCH } from '../../../../modules/nf-core/sratools/prefetch/main.nf' +include { SRATOOLS_PREFETCH } from '../../../../../modules/nf-core/sratools/prefetch/main.nf' workflow test_sratools_prefetch { diff --git a/tests/modules/nf-core/srst2/srst2/main.nf b/tests/modules/nf-core/srst2/srst2/main.nf index 27eb58a7f0f..e82f603943e 100644 --- a/tests/modules/nf-core/srst2/srst2/main.nf +++ b/tests/modules/nf-core/srst2/srst2/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SRST2_SRST2 } from '../../../../modules/nf-core/srst2/srst2/main.nf' +include { SRST2_SRST2 } from '../../../../../modules/nf-core/srst2/srst2/main.nf' workflow test_srst2_srst2_exit { diff --git a/tests/modules/nf-core/ssuissero/main.nf b/tests/modules/nf-core/ssuissero/main.nf index ff744cc3ca8..9613bc71011 100644 --- a/tests/modules/nf-core/ssuissero/main.nf +++ b/tests/modules/nf-core/ssuissero/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SSUISSERO } from '../../../modules/nf-core/ssuissero/main.nf' +include { SSUISSERO } from '../../../../modules/nf-core/ssuissero/main.nf' workflow test_ssuissero { diff --git a/tests/modules/nf-core/stadeniolib/scramble/main.nf b/tests/modules/nf-core/stadeniolib/scramble/main.nf index 15ce8382d50..9ff96fe1cde 100644 --- a/tests/modules/nf-core/stadeniolib/scramble/main.nf +++ b/tests/modules/nf-core/stadeniolib/scramble/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STADENIOLIB_SCRAMBLE } from '../../../../modules/nf-core/stadeniolib/scramble/main.nf' +include { STADENIOLIB_SCRAMBLE } from '../../../../../modules/nf-core/stadeniolib/scramble/main.nf' workflow test_stadeniolib { diff --git a/tests/modules/nf-core/staphopiasccmec/main.nf b/tests/modules/nf-core/staphopiasccmec/main.nf index 13d30a376ca..63afbcec129 100644 --- a/tests/modules/nf-core/staphopiasccmec/main.nf +++ b/tests/modules/nf-core/staphopiasccmec/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { STAPHOPIASCCMEC } from '../../../modules/nf-core/staphopiasccmec/main.nf' -include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../modules/nf-core/staphopiasccmec/main.nf' +include { STAPHOPIASCCMEC } from '../../../../modules/nf-core/staphopiasccmec/main.nf' +include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../../modules/nf-core/staphopiasccmec/main.nf' workflow test_staphopiasccmec { diff --git a/tests/modules/nf-core/star/align/main.nf b/tests/modules/nf-core/star/align/main.nf index a13e9805233..adafa76eeb6 100644 --- a/tests/modules/nf-core/star/align/main.nf +++ b/tests/modules/nf-core/star/align/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../../modules/nf-core/star/genomegenerate/main.nf' -include { STAR_ALIGN } from '../../../../modules/nf-core/star/align/main.nf' -include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/nf-core/star/align/main.nf' -include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/nf-core/star/align/main.nf' +include { STAR_GENOMEGENERATE } from '../../../../../modules/nf-core/star/genomegenerate/main.nf' +include { STAR_ALIGN } from '../../../../../modules/nf-core/star/align/main.nf' +include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../../modules/nf-core/star/align/main.nf' +include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../../modules/nf-core/star/align/main.nf' workflow test_star_alignment_single_end { input = [ diff --git a/tests/modules/nf-core/star/genomegenerate/main.nf b/tests/modules/nf-core/star/genomegenerate/main.nf index 072fc37db60..b11d32ac679 100644 --- a/tests/modules/nf-core/star/genomegenerate/main.nf +++ b/tests/modules/nf-core/star/genomegenerate/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STAR_GENOMEGENERATE } from '../../../../modules/nf-core/star/genomegenerate/main.nf' +include { STAR_GENOMEGENERATE } from '../../../../../modules/nf-core/star/genomegenerate/main.nf' workflow test_star_genomegenerate { fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) diff --git a/tests/modules/nf-core/stranger/main.nf b/tests/modules/nf-core/stranger/main.nf index edd977947fd..492c886990d 100644 --- a/tests/modules/nf-core/stranger/main.nf +++ b/tests/modules/nf-core/stranger/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { EXPANSIONHUNTER } from '../../../modules/nf-core/expansionhunter/main.nf' -include { STRANGER } from '../../../modules/nf-core/stranger/main.nf' +include { EXPANSIONHUNTER } from '../../../../modules/nf-core/expansionhunter/main.nf' +include { STRANGER } from '../../../../modules/nf-core/stranger/main.nf' input = [ [ id:'test', gender:'male' ], // meta map diff --git a/tests/modules/nf-core/strelka/germline/main.nf b/tests/modules/nf-core/strelka/germline/main.nf index c6ee89eb654..7337bc6f2fc 100644 --- a/tests/modules/nf-core/strelka/germline/main.nf +++ b/tests/modules/nf-core/strelka/germline/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRELKA_GERMLINE } from '../../../../modules/nf-core/strelka/germline/main.nf' +include { STRELKA_GERMLINE } from '../../../../../modules/nf-core/strelka/germline/main.nf' workflow test_strelka_germline { input = [ diff --git a/tests/modules/nf-core/strelka/somatic/main.nf b/tests/modules/nf-core/strelka/somatic/main.nf index 0d796f3f4e2..d11e372f9aa 100644 --- a/tests/modules/nf-core/strelka/somatic/main.nf +++ b/tests/modules/nf-core/strelka/somatic/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRELKA_SOMATIC } from '../../../../modules/nf-core/strelka/somatic/main.nf' +include { STRELKA_SOMATIC } from '../../../../../modules/nf-core/strelka/somatic/main.nf' workflow test_strelka_somatic { diff --git a/tests/modules/nf-core/stringtie/merge/main.nf b/tests/modules/nf-core/stringtie/merge/main.nf index 86c5ba1c0de..1395bc8b148 100644 --- a/tests/modules/nf-core/stringtie/merge/main.nf +++ b/tests/modules/nf-core/stringtie/merge/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { STRINGTIE_STRINGTIE } from '../../../../modules/nf-core/stringtie/stringtie/main.nf' -include { STRINGTIE_MERGE } from '../../../../modules/nf-core/stringtie/merge/main.nf' +include { STRINGTIE_STRINGTIE } from '../../../../../modules/nf-core/stringtie/stringtie/main.nf' +include { STRINGTIE_MERGE } from '../../../../../modules/nf-core/stringtie/merge/main.nf' /* * Test with forward strandedness diff --git a/tests/modules/nf-core/stringtie/stringtie/main.nf b/tests/modules/nf-core/stringtie/stringtie/main.nf index 633877714a7..b95ddfca0e3 100644 --- a/tests/modules/nf-core/stringtie/stringtie/main.nf +++ b/tests/modules/nf-core/stringtie/stringtie/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { STRINGTIE_STRINGTIE } from '../../../../modules/nf-core/stringtie/stringtie/main.nf' +include { STRINGTIE_STRINGTIE } from '../../../../../modules/nf-core/stringtie/stringtie/main.nf' // // Test with forward strandedness // diff --git a/tests/modules/nf-core/subread/featurecounts/main.nf b/tests/modules/nf-core/subread/featurecounts/main.nf index 722debaa614..1cc38b1115f 100644 --- a/tests/modules/nf-core/subread/featurecounts/main.nf +++ b/tests/modules/nf-core/subread/featurecounts/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SUBREAD_FEATURECOUNTS } from '../../../../modules/nf-core/subread/featurecounts/main.nf' +include { SUBREAD_FEATURECOUNTS } from '../../../../../modules/nf-core/subread/featurecounts/main.nf' workflow test_subread_featurecounts_forward { diff --git a/tests/modules/nf-core/svdb/merge/main.nf b/tests/modules/nf-core/svdb/merge/main.nf index f320df78507..ddf64479a6e 100644 --- a/tests/modules/nf-core/svdb/merge/main.nf +++ b/tests/modules/nf-core/svdb/merge/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SVDB_MERGE } from '../../../../modules/nf-core/svdb/merge/main.nf' +include { SVDB_MERGE } from '../../../../../modules/nf-core/svdb/merge/main.nf' workflow test_svdb_merge { diff --git a/tests/modules/nf-core/svdb/query/main.nf b/tests/modules/nf-core/svdb/query/main.nf index 66b37d14096..136dd5e0395 100644 --- a/tests/modules/nf-core/svdb/query/main.nf +++ b/tests/modules/nf-core/svdb/query/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SVDB_QUERY } from '../../../../modules/nf-core/svdb/query/main.nf' +include { SVDB_QUERY } from '../../../../../modules/nf-core/svdb/query/main.nf' workflow test_svdb_query { diff --git a/tests/modules/nf-core/svtk/standardize/main.nf b/tests/modules/nf-core/svtk/standardize/main.nf index 97a1b3d14aa..0964ace0684 100644 --- a/tests/modules/nf-core/svtk/standardize/main.nf +++ b/tests/modules/nf-core/svtk/standardize/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { SVTK_STANDARDIZE } from '../../../../modules/nf-core/svtk/standardize/main.nf' -include { MANTA_GERMLINE } from '../../../../modules/nf-core/manta/germline/main.nf' +include { SVTK_STANDARDIZE } from '../../../../../modules/nf-core/svtk/standardize/main.nf' +include { MANTA_GERMLINE } from '../../../../../modules/nf-core/manta/germline/main.nf' workflow test_svtk_standardize { diff --git a/tests/modules/nf-core/tabix/bgzip/main.nf b/tests/modules/nf-core/tabix/bgzip/main.nf index 65c6ba1ce15..2e407090fc0 100644 --- a/tests/modules/nf-core/tabix/bgzip/main.nf +++ b/tests/modules/nf-core/tabix/bgzip/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { TABIX_BGZIP } from '../../../../modules/nf-core/tabix/bgzip/main.nf' -include { TABIX_BGZIP as TABIX_BGZIP_WITH_GZI } from '../../../../modules/nf-core/tabix/bgzip/main.nf' +include { TABIX_BGZIP } from '../../../../../modules/nf-core/tabix/bgzip/main.nf' +include { TABIX_BGZIP as TABIX_BGZIP_WITH_GZI } from '../../../../../modules/nf-core/tabix/bgzip/main.nf' workflow test_tabix_bgzip_compress { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/tabix/bgziptabix/main.nf b/tests/modules/nf-core/tabix/bgziptabix/main.nf index f9eec7e2507..26e17101f8b 100644 --- a/tests/modules/nf-core/tabix/bgziptabix/main.nf +++ b/tests/modules/nf-core/tabix/bgziptabix/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TABIX_BGZIPTABIX } from '../../../../modules/nf-core/tabix/bgziptabix/main.nf' +include { TABIX_BGZIPTABIX } from '../../../../../modules/nf-core/tabix/bgziptabix/main.nf' workflow test_tabix_bgziptabix { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/tabix/tabix/main.nf b/tests/modules/nf-core/tabix/tabix/main.nf index 1653e60173f..1eb7bacff9d 100644 --- a/tests/modules/nf-core/tabix/tabix/main.nf +++ b/tests/modules/nf-core/tabix/tabix/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { TABIX_TABIX as TABIX_BED } from '../../../../modules/nf-core/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/nf-core/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/nf-core/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_BED } from '../../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_GFF } from '../../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../../modules/nf-core/tabix/tabix/main.nf' workflow test_tabix_tabix_bed { input = [ [ id:'B.bed' ], // meta map diff --git a/tests/modules/nf-core/tailfindr/main.nf b/tests/modules/nf-core/tailfindr/main.nf index 2102527fda0..c9e109cba71 100644 --- a/tests/modules/nf-core/tailfindr/main.nf +++ b/tests/modules/nf-core/tailfindr/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TAILFINDR } from '../../../modules/nf-core/tailfindr/main.nf' +include { TAILFINDR } from '../../../../modules/nf-core/tailfindr/main.nf' workflow test_tailfindr { diff --git a/tests/modules/nf-core/tbprofiler/profile/main.nf b/tests/modules/nf-core/tbprofiler/profile/main.nf index 8495f6b7ed8..00b1feb4ee1 100644 --- a/tests/modules/nf-core/tbprofiler/profile/main.nf +++ b/tests/modules/nf-core/tbprofiler/profile/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TBPROFILER_PROFILE } from '../../../../modules/nf-core/tbprofiler/profile/main.nf' +include { TBPROFILER_PROFILE } from '../../../../../modules/nf-core/tbprofiler/profile/main.nf' workflow test_tbprofiler_profile_illumina { diff --git a/tests/modules/nf-core/tiddit/cov/main.nf b/tests/modules/nf-core/tiddit/cov/main.nf index eea0b027c56..fccb515d64b 100644 --- a/tests/modules/nf-core/tiddit/cov/main.nf +++ b/tests/modules/nf-core/tiddit/cov/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/nf-core/tiddit/cov/main.nf' -include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/nf-core/tiddit/cov/main.nf' +include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../../modules/nf-core/tiddit/cov/main.nf' +include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../../modules/nf-core/tiddit/cov/main.nf' workflow test_tiddit_cov_cram_bed { diff --git a/tests/modules/nf-core/tiddit/sv/main.nf b/tests/modules/nf-core/tiddit/sv/main.nf index ff08f3dfb07..04d88c9dd10 100644 --- a/tests/modules/nf-core/tiddit/sv/main.nf +++ b/tests/modules/nf-core/tiddit/sv/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' -include { TIDDIT_SV } from '../../../../modules/nf-core/tiddit/sv/main.nf' -include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/nf-core/tiddit/sv/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' +include { TIDDIT_SV } from '../../../../../modules/nf-core/tiddit/sv/main.nf' +include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../../modules/nf-core/tiddit/sv/main.nf' workflow test_tiddit_sv_bam { input = [ diff --git a/tests/modules/nf-core/transdecoder/longorf/main.nf b/tests/modules/nf-core/transdecoder/longorf/main.nf index 6375ef7a724..1877d9ee8fd 100644 --- a/tests/modules/nf-core/transdecoder/longorf/main.nf +++ b/tests/modules/nf-core/transdecoder/longorf/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TRANSDECODER_LONGORF } from '../../../../modules/nf-core/transdecoder/longorf/main.nf' +include { TRANSDECODER_LONGORF } from '../../../../../modules/nf-core/transdecoder/longorf/main.nf' workflow test_transdecoder_longorf { diff --git a/tests/modules/nf-core/transdecoder/predict/main.nf b/tests/modules/nf-core/transdecoder/predict/main.nf index dbb6c021f30..2a085151e74 100644 --- a/tests/modules/nf-core/transdecoder/predict/main.nf +++ b/tests/modules/nf-core/transdecoder/predict/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { TRANSDECODER_PREDICT } from '../../../../modules/nf-core/transdecoder/predict/main.nf' -include { TRANSDECODER_LONGORF } from '../../../../modules/nf-core/transdecoder/longorf/main.nf' +include { TRANSDECODER_PREDICT } from '../../../../../modules/nf-core/transdecoder/predict/main.nf' +include { TRANSDECODER_LONGORF } from '../../../../../modules/nf-core/transdecoder/longorf/main.nf' workflow test_transdecoder_predict { diff --git a/tests/modules/nf-core/trimgalore/main.nf b/tests/modules/nf-core/trimgalore/main.nf index db87ce77ea4..6c09dcb7f1a 100644 --- a/tests/modules/nf-core/trimgalore/main.nf +++ b/tests/modules/nf-core/trimgalore/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { TRIMGALORE } from '../../../modules/nf-core/trimgalore/main.nf' +include { TRIMGALORE } from '../../../../modules/nf-core/trimgalore/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/trimmomatic/main.nf b/tests/modules/nf-core/trimmomatic/main.nf index 9cd54fbddcb..0114743e225 100644 --- a/tests/modules/nf-core/trimmomatic/main.nf +++ b/tests/modules/nf-core/trimmomatic/main.nf @@ -4,7 +4,7 @@ include { TRIMMOMATIC as TRIMMOMATIC_SE TRIMMOMATIC as TRIMMOMATIC_PE TRIMMOMATIC -} from '../../../modules/nf-core/trimmomatic/main.nf' +} from '../../../../modules/nf-core/trimmomatic/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/ucsc/bedclip/main.nf b/tests/modules/nf-core/ucsc/bedclip/main.nf index e6a5049df2c..df0dabe28a7 100755 --- a/tests/modules/nf-core/ucsc/bedclip/main.nf +++ b/tests/modules/nf-core/ucsc/bedclip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDCLIP } from '../../../../modules/nf-core/ucsc/bedclip/main.nf' +include { UCSC_BEDCLIP } from '../../../../../modules/nf-core/ucsc/bedclip/main.nf' workflow test_ucsc_bedclip { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 5dade993f6e..de7efec6f06 100644 --- a/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/tests/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../modules/nf-core/ucsc/bedgraphtobigwig/main.nf' +include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../../modules/nf-core/ucsc/bedgraphtobigwig/main.nf' workflow test_ucsc_bedgraphtobigwig { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/ucsc/bedtobigbed/main.nf b/tests/modules/nf-core/ucsc/bedtobigbed/main.nf index 03de60c21fe..07708297697 100644 --- a/tests/modules/nf-core/ucsc/bedtobigbed/main.nf +++ b/tests/modules/nf-core/ucsc/bedtobigbed/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UCSC_BEDTOBIGBED } from '../../../../modules/nf-core/ucsc/bedtobigbed/main.nf' -include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../modules/nf-core/ucsc/bedtobigbed/main.nf' +include { UCSC_BEDTOBIGBED } from '../../../../../modules/nf-core/ucsc/bedtobigbed/main.nf' +include { UCSC_BEDTOBIGBED as UCSC_BEDTOBIGBED_AS } from '../../../../../modules/nf-core/ucsc/bedtobigbed/main.nf' workflow test_ucsc_bedtobigbed { input = [ [ id: 'test' ], // meta map diff --git a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf index f48ff39a05f..771bf066e8e 100644 --- a/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf +++ b/tests/modules/nf-core/ucsc/bigwigaverageoverbed/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/nf-core/ucsc/bigwigaverageoverbed/main.nf' +include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../../modules/nf-core/ucsc/bigwigaverageoverbed/main.nf' workflow test_ucsc_bigwigaverageoverbed { input = [ diff --git a/tests/modules/nf-core/ucsc/liftover/main.nf b/tests/modules/nf-core/ucsc/liftover/main.nf index 9ee2e472483..87b4f6d47cb 100644 --- a/tests/modules/nf-core/ucsc/liftover/main.nf +++ b/tests/modules/nf-core/ucsc/liftover/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_LIFTOVER } from '../../../../modules/nf-core/ucsc/liftover/main.nf' +include { UCSC_LIFTOVER } from '../../../../../modules/nf-core/ucsc/liftover/main.nf' workflow test_ucsc_liftover { diff --git a/tests/modules/nf-core/ucsc/wigtobigwig/main.nf b/tests/modules/nf-core/ucsc/wigtobigwig/main.nf index 33e23937dc3..2f5558987bc 100644 --- a/tests/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/tests/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UCSC_WIGTOBIGWIG } from '../../../../modules/nf-core/ucsc/wigtobigwig/main.nf' +include { UCSC_WIGTOBIGWIG } from '../../../../../modules/nf-core/ucsc/wigtobigwig/main.nf' workflow test_ucsc_wigtobigwig { diff --git a/tests/modules/nf-core/ultra/align/main.nf b/tests/modules/nf-core/ultra/align/main.nf index 2d5bba382f7..ff40ed1acdf 100644 --- a/tests/modules/nf-core/ultra/align/main.nf +++ b/tests/modules/nf-core/ultra/align/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' -include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' -include { ULTRA_INDEX } from '../../../../modules/nf-core/ultra/index/main.nf' -include { ULTRA_ALIGN } from '../../../../modules/nf-core/ultra/align/main.nf' +include { GUNZIP } from '../../../../../modules/nf-core/gunzip/main.nf' +include { GFFREAD } from '../../../../../modules/nf-core/gffread/main.nf' +include { ULTRA_INDEX } from '../../../../../modules/nf-core/ultra/index/main.nf' +include { ULTRA_ALIGN } from '../../../../../modules/nf-core/ultra/align/main.nf' workflow test_ultra_align { diff --git a/tests/modules/nf-core/ultra/index/main.nf b/tests/modules/nf-core/ultra/index/main.nf index ce98ee7922d..e5df61e6c44 100644 --- a/tests/modules/nf-core/ultra/index/main.nf +++ b/tests/modules/nf-core/ultra/index/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { ULTRA_INDEX } from '../../../../modules/nf-core/ultra/index/main.nf' -include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' +include { ULTRA_INDEX } from '../../../../../modules/nf-core/ultra/index/main.nf' +include { GFFREAD } from '../../../../../modules/nf-core/gffread/main.nf' workflow test_ultra_index { diff --git a/tests/modules/nf-core/ultra/pipeline/main.nf b/tests/modules/nf-core/ultra/pipeline/main.nf index dcd3bc4d585..fe0487e4417 100644 --- a/tests/modules/nf-core/ultra/pipeline/main.nf +++ b/tests/modules/nf-core/ultra/pipeline/main.nf @@ -2,9 +2,9 @@ nextflow.enable.dsl = 2 -include { ULTRA_PIPELINE } from '../../../../modules/nf-core/ultra/pipeline/main.nf' -include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf' -include { GFFREAD } from '../../../../modules/nf-core/gffread/main.nf' +include { ULTRA_PIPELINE } from '../../../../../modules/nf-core/ultra/pipeline/main.nf' +include { GUNZIP } from '../../../../../modules/nf-core/gunzip/main.nf' +include { GFFREAD } from '../../../../../modules/nf-core/gffread/main.nf' workflow test_ultra_pipeline { diff --git a/tests/modules/nf-core/umitools/dedup/main.nf b/tests/modules/nf-core/umitools/dedup/main.nf index 6478d619c78..2a9b6af1ba4 100644 --- a/tests/modules/nf-core/umitools/dedup/main.nf +++ b/tests/modules/nf-core/umitools/dedup/main.nf @@ -2,11 +2,11 @@ nextflow.enable.dsl = 2 -include { UMITOOLS_EXTRACT } from '../../../../modules/nf-core/umitools/extract/main.nf' -include { BWA_INDEX } from '../../../../modules/nf-core/bwa/index/main.nf' -include { BWA_MEM } from '../../../../modules/nf-core/bwa/mem/main.nf' -include { SAMTOOLS_INDEX } from '../../../../modules/nf-core/samtools/index/main.nf' -include { UMITOOLS_DEDUP } from '../../../../modules/nf-core/umitools/dedup/main.nf' +include { UMITOOLS_EXTRACT } from '../../../../../modules/nf-core/umitools/extract/main.nf' +include { BWA_INDEX } from '../../../../../modules/nf-core/bwa/index/main.nf' +include { BWA_MEM } from '../../../../../modules/nf-core/bwa/mem/main.nf' +include { SAMTOOLS_INDEX } from '../../../../../modules/nf-core/samtools/index/main.nf' +include { UMITOOLS_DEDUP } from '../../../../../modules/nf-core/umitools/dedup/main.nf' // // Test with no UMI diff --git a/tests/modules/nf-core/umitools/extract/main.nf b/tests/modules/nf-core/umitools/extract/main.nf index b6301eece75..417cc70f077 100644 --- a/tests/modules/nf-core/umitools/extract/main.nf +++ b/tests/modules/nf-core/umitools/extract/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UMITOOLS_EXTRACT } from '../../../../modules/nf-core/umitools/extract/main.nf' +include { UMITOOLS_EXTRACT } from '../../../../../modules/nf-core/umitools/extract/main.nf' // // Test with single-end data diff --git a/tests/modules/nf-core/unicycler/main.nf b/tests/modules/nf-core/unicycler/main.nf index c430a56efa9..0c7c037b6d0 100644 --- a/tests/modules/nf-core/unicycler/main.nf +++ b/tests/modules/nf-core/unicycler/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UNICYCLER } from '../../../modules/nf-core/unicycler/main.nf' +include { UNICYCLER } from '../../../../modules/nf-core/unicycler/main.nf' workflow test_unicycler_single_end { input = [ [ id:'test', single_end:true ], // meta map diff --git a/tests/modules/nf-core/untar/main.nf b/tests/modules/nf-core/untar/main.nf index 698f39e299e..3d92298bc0f 100644 --- a/tests/modules/nf-core/untar/main.nf +++ b/tests/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_untar { input = [ diff --git a/tests/modules/nf-core/unzip/main.nf b/tests/modules/nf-core/unzip/main.nf index f20ad35d9c4..7992797b59e 100644 --- a/tests/modules/nf-core/unzip/main.nf +++ b/tests/modules/nf-core/unzip/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { UNZIP } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf' workflow test_unzip { diff --git a/tests/modules/nf-core/vardictjava/main.nf b/tests/modules/nf-core/vardictjava/main.nf index 0267bb4ee57..5c199a844e1 100644 --- a/tests/modules/nf-core/vardictjava/main.nf +++ b/tests/modules/nf-core/vardictjava/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VARDICTJAVA } from '../../../modules/nf-core/vardictjava/main.nf' +include { VARDICTJAVA } from '../../../../modules/nf-core/vardictjava/main.nf' workflow test_vardictjava_bam { diff --git a/tests/modules/nf-core/variantbam/main.nf b/tests/modules/nf-core/variantbam/main.nf index 150e8e4c061..8adbee3fac9 100644 --- a/tests/modules/nf-core/variantbam/main.nf +++ b/tests/modules/nf-core/variantbam/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VARIANTBAM } from '../../../modules/nf-core/variantbam/main.nf' +include { VARIANTBAM } from '../../../../modules/nf-core/variantbam/main.nf' workflow test_variantbam { diff --git a/tests/modules/nf-core/vcf2db/main.nf b/tests/modules/nf-core/vcf2db/main.nf index 6ff2a64f570..6ea67bbbfa3 100644 --- a/tests/modules/nf-core/vcf2db/main.nf +++ b/tests/modules/nf-core/vcf2db/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VCF2DB } from '../../../modules/nf-core/vcf2db/main.nf' +include { VCF2DB } from '../../../../modules/nf-core/vcf2db/main.nf' workflow test_vcf2db { diff --git a/tests/modules/nf-core/vcf2maf/main.nf b/tests/modules/nf-core/vcf2maf/main.nf index 7d51739c786..8deed5cf74a 100644 --- a/tests/modules/nf-core/vcf2maf/main.nf +++ b/tests/modules/nf-core/vcf2maf/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { VCF2MAF } from '../../../modules/nf-core/vcf2maf/main.nf' -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' +include { VCF2MAF } from '../../../../modules/nf-core/vcf2maf/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' workflow test_vcf2maf_no_vep { diff --git a/tests/modules/nf-core/vcfanno/main.nf b/tests/modules/nf-core/vcfanno/main.nf index 6f744be342a..3fdfe71eb8b 100644 --- a/tests/modules/nf-core/vcfanno/main.nf +++ b/tests/modules/nf-core/vcfanno/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { UNTAR } from '../../../modules/nf-core/untar/main.nf' -include { VCFANNO } from '../../../modules/nf-core/vcfanno/main.nf' +include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' +include { VCFANNO } from '../../../../modules/nf-core/vcfanno/main.nf' workflow test_vcfanno { diff --git a/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf b/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf index 22703141a3d..1f8cd39f07b 100644 --- a/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf +++ b/tests/modules/nf-core/vcflib/vcfbreakmulti/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VCFLIB_VCFBREAKMULTI } from '../../../../modules/nf-core/vcflib/vcfbreakmulti/main.nf' +include { VCFLIB_VCFBREAKMULTI } from '../../../../../modules/nf-core/vcflib/vcfbreakmulti/main.nf' workflow test_vcflib_vcfbreakmulti { diff --git a/tests/modules/nf-core/vcflib/vcfuniq/main.nf b/tests/modules/nf-core/vcflib/vcfuniq/main.nf index d920d97d39b..b355301e5a1 100644 --- a/tests/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/tests/modules/nf-core/vcflib/vcfuniq/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VCFLIB_VCFUNIQ } from '../../../../modules/nf-core/vcflib/vcfuniq/main.nf' +include { VCFLIB_VCFUNIQ } from '../../../../../modules/nf-core/vcflib/vcfuniq/main.nf' workflow test_vcflib_vcfuniq { diff --git a/tests/modules/nf-core/vcftools/main.nf b/tests/modules/nf-core/vcftools/main.nf index a7659f3b143..d1e49cb3618 100644 --- a/tests/modules/nf-core/vcftools/main.nf +++ b/tests/modules/nf-core/vcftools/main.nf @@ -2,8 +2,8 @@ nextflow.enable.dsl = 2 -include { VCFTOOLS as VCFTOOLS_BASE } from '../../../modules/nf-core/vcftools/main.nf' -include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/nf-core/vcftools/main.nf' +include { VCFTOOLS as VCFTOOLS_BASE } from '../../../../modules/nf-core/vcftools/main.nf' +include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../../modules/nf-core/vcftools/main.nf' workflow test_vcftools_vcf_base { input = [ [ id:'test' ], // meta map diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf b/tests/modules/nf-core/vsearch/sintax/main.nf index 0f80c599c7e..59e551bca79 100644 --- a/tests/modules/nf-core/vsearch/sintax/main.nf +++ b/tests/modules/nf-core/vsearch/sintax/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VSEARCH_SINTAX } from '../../../../modules/nf-core/vsearch/sintax/main.nf' +include { VSEARCH_SINTAX } from '../../../../../modules/nf-core/vsearch/sintax/main.nf' workflow test_vsearch_sintax { diff --git a/tests/modules/nf-core/vsearch/usearchglobal/main.nf b/tests/modules/nf-core/vsearch/usearchglobal/main.nf index 252269136c7..925f0cb2ac3 100644 --- a/tests/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/tests/modules/nf-core/vsearch/usearchglobal/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { VSEARCH_USEARCHGLOBAL } from '../../../../modules/nf-core/vsearch/usearchglobal/main.nf' +include { VSEARCH_USEARCHGLOBAL } from '../../../../../modules/nf-core/vsearch/usearchglobal/main.nf' workflow test_vsearch_usearchglobal { diff --git a/tests/modules/nf-core/whamg/main.nf b/tests/modules/nf-core/whamg/main.nf index 22e8ab7b643..3301b194d43 100644 --- a/tests/modules/nf-core/whamg/main.nf +++ b/tests/modules/nf-core/whamg/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { WHAMG } from '../../../modules/nf-core/whamg/main.nf' +include { WHAMG } from '../../../../modules/nf-core/whamg/main.nf' workflow test_whamg_bam { diff --git a/tests/modules/nf-core/yara/index/main.nf b/tests/modules/nf-core/yara/index/main.nf index c0de4cd844f..32a8efef899 100644 --- a/tests/modules/nf-core/yara/index/main.nf +++ b/tests/modules/nf-core/yara/index/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { YARA_INDEX } from '../../../../modules/nf-core/yara/index/main.nf' +include { YARA_INDEX } from '../../../../../modules/nf-core/yara/index/main.nf' workflow test_yara_index { diff --git a/tests/modules/nf-core/yara/mapper/main.nf b/tests/modules/nf-core/yara/mapper/main.nf index 3279c3c735b..a6c502d3881 100644 --- a/tests/modules/nf-core/yara/mapper/main.nf +++ b/tests/modules/nf-core/yara/mapper/main.nf @@ -3,8 +3,8 @@ nextflow.enable.dsl = 2 -include { YARA_INDEX } from '../../../../modules/nf-core/yara/index/main.nf' -include { YARA_MAPPER } from '../../../../modules/nf-core/yara/mapper/main.nf' +include { YARA_INDEX } from '../../../../../modules/nf-core/yara/index/main.nf' +include { YARA_MAPPER } from '../../../../../modules/nf-core/yara/mapper/main.nf' workflow test_yara_single_end { From b68b3b751bc9a53b56409a5819b59cd78817f611 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 3 Oct 2022 15:49:39 -0500 Subject: [PATCH 9/9] Update paths in pytest_modules.yml --- tests/config/pytest_modules.yml | 2574 +++++++++++++++---------------- 1 file changed, 1287 insertions(+), 1287 deletions(-) diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 2b1f317f3ae..2c521019087 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,2545 +1,2545 @@ abacas: - - modules/abacas/** - - tests/modules/abacas/** + - modules/nf-core/abacas/** + - tests/modules/nf-core/abacas/** abricate/run: - - modules/abricate/run/** - - tests/modules/abricate/run/** + - modules/nf-core/abricate/run/** + - tests/modules/nf-core/abricate/run/** abricate/summary: - - modules/abricate/summary/** - - tests/modules/abricate/summary/** + - modules/nf-core/abricate/summary/** + - tests/modules/nf-core/abricate/summary/** adapterremoval: - - modules/adapterremoval/** - - tests/modules/adapterremoval/** + - modules/nf-core/adapterremoval/** + - tests/modules/nf-core/adapterremoval/** adapterremovalfixprefix: - - modules/adapterremovalfixprefix/** - - tests/modules/adapterremovalfixprefix/** + - modules/nf-core/adapterremovalfixprefix/** + - tests/modules/nf-core/adapterremovalfixprefix/** agrvate: - - modules/agrvate/** - - tests/modules/agrvate/** + - modules/nf-core/agrvate/** + - tests/modules/nf-core/agrvate/** allelecounter: - - modules/allelecounter/** - - tests/modules/allelecounter/** + - modules/nf-core/allelecounter/** + - tests/modules/nf-core/allelecounter/** ampir: - - modules/ampir/** - - tests/modules/ampir/** + - modules/nf-core/ampir/** + - tests/modules/nf-core/ampir/** amplify/predict: - - modules/amplify/predict/** - - tests/modules/amplify/predict/** + - modules/nf-core/amplify/predict/** + - tests/modules/nf-core/amplify/predict/** amps: - - modules/amps/** - - tests/modules/amps/** + - modules/nf-core/amps/** + - tests/modules/nf-core/amps/** amrfinderplus/run: - - modules/amrfinderplus/run/** - - tests/modules/amrfinderplus/run/** + - modules/nf-core/amrfinderplus/run/** + - tests/modules/nf-core/amrfinderplus/run/** amrfinderplus/update: - - modules/amrfinderplus/update/** - - tests/modules/amrfinderplus/update/** + - modules/nf-core/amrfinderplus/update/** + - tests/modules/nf-core/amrfinderplus/update/** angsd/docounts: - - modules/angsd/docounts/** - - tests/modules/angsd/docounts/** + - modules/nf-core/angsd/docounts/** + - tests/modules/nf-core/angsd/docounts/** antismash/antismashlite: - - modules/antismash/antismashlite/** - - tests/modules/antismash/antismashlite/** + - modules/nf-core/antismash/antismashlite/** + - tests/modules/nf-core/antismash/antismashlite/** antismash/antismashlitedownloaddatabases: - - modules/antismash/antismashlitedownloaddatabases/** - - tests/modules/antismash/antismashlitedownloaddatabases/** + - modules/nf-core/antismash/antismashlitedownloaddatabases/** + - tests/modules/nf-core/antismash/antismashlitedownloaddatabases/** ariba/getref: - - modules/ariba/getref/** - - tests/modules/ariba/getref/** + - modules/nf-core/ariba/getref/** + - tests/modules/nf-core/ariba/getref/** ariba/run: - - modules/ariba/run/** - - tests/modules/ariba/run/** + - modules/nf-core/ariba/run/** + - tests/modules/nf-core/ariba/run/** arriba: - - modules/arriba/** - - tests/modules/arriba/** + - modules/nf-core/arriba/** + - tests/modules/nf-core/arriba/** artic/guppyplex: - - modules/artic/guppyplex/** - - tests/modules/artic/guppyplex/** + - modules/nf-core/artic/guppyplex/** + - tests/modules/nf-core/artic/guppyplex/** artic/minion: - - modules/artic/minion/** - - tests/modules/artic/minion/** + - modules/nf-core/artic/minion/** + - tests/modules/nf-core/artic/minion/** ascat: - - modules/ascat/** - - tests/modules/ascat/** + - modules/nf-core/ascat/** + - tests/modules/nf-core/ascat/** assemblyscan: - - modules/assemblyscan/** - - tests/modules/assemblyscan/** + - modules/nf-core/assemblyscan/** + - tests/modules/nf-core/assemblyscan/** ataqv/ataqv: - - modules/ataqv/ataqv/** - - tests/modules/ataqv/ataqv/** + - modules/nf-core/ataqv/ataqv/** + - tests/modules/nf-core/ataqv/ataqv/** ataqv/mkarv: - - modules/ataqv/mkarv/** - - tests/modules/ataqv/mkarv/** + - modules/nf-core/ataqv/mkarv/** + - tests/modules/nf-core/ataqv/mkarv/** atlas/call: - - modules/atlas/call/** - - tests/modules/atlas/call/** + - modules/nf-core/atlas/call/** + - tests/modules/nf-core/atlas/call/** atlas/pmd: - - modules/atlas/pmd/** - - tests/modules/atlas/pmd/** + - modules/nf-core/atlas/pmd/** + - tests/modules/nf-core/atlas/pmd/** atlas/recal: - - modules/atlas/recal/** - - tests/modules/atlas/recal/** + - modules/nf-core/atlas/recal/** + - tests/modules/nf-core/atlas/recal/** atlas/splitmerge: - - modules/atlas/splitmerge/** - - tests/modules/atlas/splitmerge/** + - modules/nf-core/atlas/splitmerge/** + - tests/modules/nf-core/atlas/splitmerge/** bakta: - - modules/bakta/** - - tests/modules/bakta/** + - modules/nf-core/bakta/** + - tests/modules/nf-core/bakta/** bamaligncleaner: - - modules/bamaligncleaner/** - - tests/modules/bamaligncleaner/** + - modules/nf-core/bamaligncleaner/** + - tests/modules/nf-core/bamaligncleaner/** bamcmp: - - modules/bamcmp/** - - tests/modules/bamcmp/** + - modules/nf-core/bamcmp/** + - tests/modules/nf-core/bamcmp/** bamtools/convert: - - modules/bamtools/convert/** - - tests/modules/bamtools/convert/** + - modules/nf-core/bamtools/convert/** + - tests/modules/nf-core/bamtools/convert/** bamtools/split: - - modules/bamtools/split/** - - tests/modules/bamtools/split/** + - modules/nf-core/bamtools/split/** + - tests/modules/nf-core/bamtools/split/** bamtools/stats: - - modules/bamtools/stats/** - - tests/modules/bamtools/stats/** + - modules/nf-core/bamtools/stats/** + - tests/modules/nf-core/bamtools/stats/** bamutil/trimbam: - - modules/bamutil/trimbam/** - - tests/modules/bamutil/trimbam/** + - modules/nf-core/bamutil/trimbam/** + - tests/modules/nf-core/bamutil/trimbam/** bandage/image: - - modules/bandage/image/** - - tests/modules/bandage/image/** + - modules/nf-core/bandage/image/** + - tests/modules/nf-core/bandage/image/** bases2fastq: - - modules/bases2fastq/** - - tests/modules/bases2fastq/** + - modules/nf-core/bases2fastq/** + - tests/modules/nf-core/bases2fastq/** bbmap/align: - - modules/bbmap/align/** - - tests/modules/bbmap/align/** + - modules/nf-core/bbmap/align/** + - tests/modules/nf-core/bbmap/align/** bbmap/bbduk: - - modules/bbmap/bbduk/** - - tests/modules/bbmap/bbduk/** + - modules/nf-core/bbmap/bbduk/** + - tests/modules/nf-core/bbmap/bbduk/** bbmap/bbsplit: - - modules/bbmap/bbsplit/** - - tests/modules/bbmap/bbsplit/** + - modules/nf-core/bbmap/bbsplit/** + - tests/modules/nf-core/bbmap/bbsplit/** bbmap/clumpify: - - modules/bbmap/clumpify/** - - tests/modules/bbmap/clumpify/** + - modules/nf-core/bbmap/clumpify/** + - tests/modules/nf-core/bbmap/clumpify/** bbmap/index: - - modules/bbmap/index/** - - tests/modules/bbmap/index/** + - modules/nf-core/bbmap/index/** + - tests/modules/nf-core/bbmap/index/** bbmap/pileup: - - modules/bbmap/pileup/** - - tests/modules/bbmap/pileup/** + - modules/nf-core/bbmap/pileup/** + - tests/modules/nf-core/bbmap/pileup/** bcftools/annotate: - - modules/bcftools/annotate/** - - tests/modules/bcftools/annotate/** + - modules/nf-core/bcftools/annotate/** + - tests/modules/nf-core/bcftools/annotate/** bcftools/concat: - - modules/bcftools/concat/** - - tests/modules/bcftools/concat/** + - modules/nf-core/bcftools/concat/** + - tests/modules/nf-core/bcftools/concat/** bcftools/consensus: - - modules/bcftools/consensus/** - - tests/modules/bcftools/consensus/** + - modules/nf-core/bcftools/consensus/** + - tests/modules/nf-core/bcftools/consensus/** bcftools/convert: - - modules/bcftools/convert/** - - tests/modules/bcftools/convert/** + - modules/nf-core/bcftools/convert/** + - tests/modules/nf-core/bcftools/convert/** bcftools/filter: - - modules/bcftools/filter/** - - tests/modules/bcftools/filter/** + - modules/nf-core/bcftools/filter/** + - tests/modules/nf-core/bcftools/filter/** bcftools/index: - - modules/bcftools/index/** - - tests/modules/bcftools/index** + - modules/nf-core/bcftools/index/** + - tests/modules/nf-core/bcftools/index** bcftools/isec: - - modules/bcftools/isec/** - - tests/modules/bcftools/isec/** + - modules/nf-core/bcftools/isec/** + - tests/modules/nf-core/bcftools/isec/** bcftools/merge: - - modules/bcftools/merge/** - - tests/modules/bcftools/merge/** + - modules/nf-core/bcftools/merge/** + - tests/modules/nf-core/bcftools/merge/** bcftools/mpileup: - - modules/bcftools/mpileup/** - - tests/modules/bcftools/mpileup/** + - modules/nf-core/bcftools/mpileup/** + - tests/modules/nf-core/bcftools/mpileup/** bcftools/norm: - - modules/bcftools/norm/** - - tests/modules/bcftools/norm/** + - modules/nf-core/bcftools/norm/** + - tests/modules/nf-core/bcftools/norm/** bcftools/query: - - modules/bcftools/query/** - - tests/modules/bcftools/query/** + - modules/nf-core/bcftools/query/** + - tests/modules/nf-core/bcftools/query/** bcftools/reheader: - - modules/bcftools/reheader/** - - tests/modules/bcftools/reheader/** + - modules/nf-core/bcftools/reheader/** + - tests/modules/nf-core/bcftools/reheader/** bcftools/roh: - - modules/bcftools/roh/** - - tests/modules/bcftools/roh/** + - modules/nf-core/bcftools/roh/** + - tests/modules/nf-core/bcftools/roh/** bcftools/sort: - - modules/bcftools/sort/** - - tests/modules/bcftools/sort/** + - modules/nf-core/bcftools/sort/** + - tests/modules/nf-core/bcftools/sort/** bcftools/stats: - - modules/bcftools/stats/** - - tests/modules/bcftools/stats/** + - modules/nf-core/bcftools/stats/** + - tests/modules/nf-core/bcftools/stats/** bcftools/view: - - modules/bcftools/view/** - - tests/modules/bcftools/view/** + - modules/nf-core/bcftools/view/** + - tests/modules/nf-core/bcftools/view/** bcl2fastq: - - modules/bcl2fastq/** - - tests/modules/bcl2fastq/** + - modules/nf-core/bcl2fastq/** + - tests/modules/nf-core/bcl2fastq/** bclconvert: - - modules/bclconvert/** - - tests/modules/bclconvert/** + - modules/nf-core/bclconvert/** + - tests/modules/nf-core/bclconvert/** bedtools/bamtobed: - - modules/bedtools/bamtobed/** - - tests/modules/bedtools/bamtobed/** + - modules/nf-core/bedtools/bamtobed/** + - tests/modules/nf-core/bedtools/bamtobed/** bedtools/complement: - - modules/bedtools/complement/** - - tests/modules/bedtools/complement/** + - modules/nf-core/bedtools/complement/** + - tests/modules/nf-core/bedtools/complement/** bedtools/genomecov: - - modules/bedtools/genomecov/** - - tests/modules/bedtools/genomecov/** + - modules/nf-core/bedtools/genomecov/** + - tests/modules/nf-core/bedtools/genomecov/** bedtools/getfasta: - - modules/bedtools/getfasta/** - - tests/modules/bedtools/getfasta/** + - modules/nf-core/bedtools/getfasta/** + - tests/modules/nf-core/bedtools/getfasta/** bedtools/intersect: - - modules/bedtools/intersect/** - - tests/modules/bedtools/intersect/** + - modules/nf-core/bedtools/intersect/** + - tests/modules/nf-core/bedtools/intersect/** bedtools/makewindows: - - modules/bedtools/makewindows/** - - tests/modules/bedtools/makewindows/** + - modules/nf-core/bedtools/makewindows/** + - tests/modules/nf-core/bedtools/makewindows/** bedtools/maskfasta: - - modules/bedtools/maskfasta/** - - tests/modules/bedtools/maskfasta/** + - modules/nf-core/bedtools/maskfasta/** + - tests/modules/nf-core/bedtools/maskfasta/** bedtools/merge: - - modules/bedtools/merge/** - - tests/modules/bedtools/merge/** + - modules/nf-core/bedtools/merge/** + - tests/modules/nf-core/bedtools/merge/** bedtools/slop: - - modules/bedtools/slop/** - - tests/modules/bedtools/slop/** + - modules/nf-core/bedtools/slop/** + - tests/modules/nf-core/bedtools/slop/** bedtools/sort: - - modules/bedtools/sort/** - - tests/modules/bedtools/sort/** + - modules/nf-core/bedtools/sort/** + - tests/modules/nf-core/bedtools/sort/** bedtools/split: - - modules/bedtools/split/** - - tests/modules/bedtools/split/** + - modules/nf-core/bedtools/split/** + - tests/modules/nf-core/bedtools/split/** bedtools/subtract: - - modules/bedtools/subtract/** - - tests/modules/bedtools/subtract/** + - modules/nf-core/bedtools/subtract/** + - tests/modules/nf-core/bedtools/subtract/** biobambam/bammarkduplicates2: - - modules/biobambam/bammarkduplicates2/** - - tests/modules/biobambam/bammarkduplicates2/** + - modules/nf-core/biobambam/bammarkduplicates2/** + - tests/modules/nf-core/biobambam/bammarkduplicates2/** biobambam/bammerge: - - modules/biobambam/bammerge/** - - tests/modules/biobambam/bammerge/** + - modules/nf-core/biobambam/bammerge/** + - tests/modules/nf-core/biobambam/bammerge/** biobambam/bamsormadup: - - modules/biobambam/bamsormadup/** - - tests/modules/biobambam/bamsormadup/** + - modules/nf-core/biobambam/bamsormadup/** + - tests/modules/nf-core/biobambam/bamsormadup/** biscuit/align: - - modules/biscuit/index/** - - modules/biscuit/align/** - - tests/modules/biscuit/align/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/align/** + - tests/modules/nf-core/biscuit/align/** biscuit/biscuitblaster: - - modules/biscuit/index/** - - modules/biscuit/biscuitblaster/** - - tests/modules/biscuit/biscuitblaster/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/biscuitblaster/** + - tests/modules/nf-core/biscuit/biscuitblaster/** biscuit/bsconv: - - modules/biscuit/index/** - - modules/biscuit/bsconv/** - - tests/modules/biscuit/bsconv/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/bsconv/** + - tests/modules/nf-core/biscuit/bsconv/** biscuit/epiread: - - modules/biscuit/index/** - - modules/biscuit/epiread/** - - tests/modules/biscuit/epiread/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/epiread/** + - tests/modules/nf-core/biscuit/epiread/** biscuit/index: - - modules/biscuit/index/** - - tests/modules/biscuit/index/** + - modules/nf-core/biscuit/index/** + - tests/modules/nf-core/biscuit/index/** biscuit/mergecg: - - modules/biscuit/index/** - - modules/biscuit/mergecg/** - - tests/modules/biscuit/mergecg/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/mergecg/** + - tests/modules/nf-core/biscuit/mergecg/** biscuit/pileup: - - modules/biscuit/index/** - - modules/biscuit/pileup/** - - tests/modules/biscuit/pileup/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/pileup/** + - tests/modules/nf-core/biscuit/pileup/** biscuit/qc: - - modules/biscuit/index/** - - modules/biscuit/qc/** - - tests/modules/biscuit/qc/** + - modules/nf-core/biscuit/index/** + - modules/nf-core/biscuit/qc/** + - tests/modules/nf-core/biscuit/qc/** biscuit/vcf2bed: - - modules/biscuit/vcf2bed/** - - tests/modules/biscuit/vcf2bed/** + - modules/nf-core/biscuit/vcf2bed/** + - tests/modules/nf-core/biscuit/vcf2bed/** bismark/align: - - modules/bismark/align/** - - modules/bismark/genomepreparation/** - - tests/modules/bismark/align/** + - modules/nf-core/bismark/align/** + - modules/nf-core/bismark/genomepreparation/** + - tests/modules/nf-core/bismark/align/** bismark/deduplicate: - - modules/bismark/deduplicate/** - - tests/modules/bismark/deduplicate/** + - modules/nf-core/bismark/deduplicate/** + - tests/modules/nf-core/bismark/deduplicate/** bismark/genomepreparation: - - modules/bismark/genomepreparation/** - - tests/modules/bismark/genomepreparation/** + - modules/nf-core/bismark/genomepreparation/** + - tests/modules/nf-core/bismark/genomepreparation/** bismark/methylationextractor: - - modules/bismark/methylationextractor/** - - modules/bismark/genomepreparation/** - - tests/modules/bismark/methylationextractor/** + - modules/nf-core/bismark/methylationextractor/** + - modules/nf-core/bismark/genomepreparation/** + - tests/modules/nf-core/bismark/methylationextractor/** bismark/report: - - modules/bismark/genomepreparation/** - - modules/bismark/align/** - - modules/bismark/deduplicate/** - - modules/bismark/methylationextractor/** - - modules/bismark/report/** - - tests/modules/bismark/report/** + - modules/nf-core/bismark/genomepreparation/** + - modules/nf-core/bismark/align/** + - modules/nf-core/bismark/deduplicate/** + - modules/nf-core/bismark/methylationextractor/** + - modules/nf-core/bismark/report/** + - tests/modules/nf-core/bismark/report/** bismark/summary: - - modules/bismark/genomepreparation/** - - modules/bismark/align/** - - modules/bismark/deduplicate/** - - modules/bismark/methylationextractor/** - - modules/bismark/summary/** - - tests/modules/bismark/summary/** + - modules/nf-core/bismark/genomepreparation/** + - modules/nf-core/bismark/align/** + - modules/nf-core/bismark/deduplicate/** + - modules/nf-core/bismark/methylationextractor/** + - modules/nf-core/bismark/summary/** + - tests/modules/nf-core/bismark/summary/** blast/blastn: - - modules/blast/blastn/** - - tests/modules/blast/blastn/** + - modules/nf-core/blast/blastn/** + - tests/modules/nf-core/blast/blastn/** blast/makeblastdb: - - modules/blast/makeblastdb/** - - tests/modules/blast/makeblastdb/** + - modules/nf-core/blast/makeblastdb/** + - tests/modules/nf-core/blast/makeblastdb/** blast/tblastn: - - modules/blast/tblastn/** - - tests/modules/blast/tblastn/** + - modules/nf-core/blast/tblastn/** + - tests/modules/nf-core/blast/tblastn/** bowtie/align: - - modules/bowtie/align/** - - modules/bowtie/build/** - - tests/modules/bowtie/align/** + - modules/nf-core/bowtie/align/** + - modules/nf-core/bowtie/build/** + - tests/modules/nf-core/bowtie/align/** bowtie/build: - - modules/bowtie/build/** - - tests/modules/bowtie/build_test/** + - modules/nf-core/bowtie/build/** + - tests/modules/nf-core/bowtie/build_test/** bowtie2/align: - - modules/bowtie2/align/** - - modules/bowtie2/build/** - - tests/modules/bowtie2/align/** + - modules/nf-core/bowtie2/align/** + - modules/nf-core/bowtie2/build/** + - tests/modules/nf-core/bowtie2/align/** bowtie2/build: - - modules/bowtie2/build/** - - tests/modules/bowtie2/build_test/** + - modules/nf-core/bowtie2/build/** + - tests/modules/nf-core/bowtie2/build_test/** bracken/bracken: - - modules/bracken/bracken/** - - tests/modules/bracken/bracken/** + - modules/nf-core/bracken/bracken/** + - tests/modules/nf-core/bracken/bracken/** bracken/combinebrackenoutputs: - - modules/bracken/combinebrackenoutputs/** - - tests/modules/bracken/combinebrackenoutputs/** + - modules/nf-core/bracken/combinebrackenoutputs/** + - tests/modules/nf-core/bracken/combinebrackenoutputs/** busco: - - modules/busco/** - - tests/modules/busco/** + - modules/nf-core/busco/** + - tests/modules/nf-core/busco/** bwa/aln: - - modules/bwa/aln/** - - tests/modules/bwa/aln/** + - modules/nf-core/bwa/aln/** + - tests/modules/nf-core/bwa/aln/** bwa/index: - - modules/bwa/index/** - - tests/modules/bwa/index/** + - modules/nf-core/bwa/index/** + - tests/modules/nf-core/bwa/index/** bwa/mem: - - modules/bwa/mem/** - - tests/modules/bwa/mem/** + - modules/nf-core/bwa/mem/** + - tests/modules/nf-core/bwa/mem/** bwa/sampe: - - modules/bwa/sampe/** - - tests/modules/bwa/sampe/** + - modules/nf-core/bwa/sampe/** + - tests/modules/nf-core/bwa/sampe/** bwa/samse: - - modules/bwa/samse/** - - tests/modules/bwa/samse/** + - modules/nf-core/bwa/samse/** + - tests/modules/nf-core/bwa/samse/** bwamem2/index: - - modules/bwamem2/index/** - - tests/modules/bwamem2/index/** + - modules/nf-core/bwamem2/index/** + - tests/modules/nf-core/bwamem2/index/** bwamem2/mem: - - modules/bwamem2/mem/** - - tests/modules/bwamem2/mem/** + - modules/nf-core/bwamem2/mem/** + - tests/modules/nf-core/bwamem2/mem/** bwameth/align: - - modules/bwameth/align/** - - tests/modules/bwameth/align/** + - modules/nf-core/bwameth/align/** + - tests/modules/nf-core/bwameth/align/** bwameth/index: - - modules/bwameth/index/** - - tests/modules/bwameth/index/** + - modules/nf-core/bwameth/index/** + - tests/modules/nf-core/bwameth/index/** cat/cat: - - modules/cat/cat/** - - tests/modules/cat/cat/** + - modules/nf-core/cat/cat/** + - tests/modules/nf-core/cat/cat/** cat/fastq: - - modules/cat/fastq/** - - tests/modules/cat/fastq/** + - modules/nf-core/cat/fastq/** + - tests/modules/nf-core/cat/fastq/** cellranger/count: - - modules/cellranger/count/** - - tests/modules/cellranger/count/** - - modules/cellranger/mkref/** - - tests/modules/cellranger/mkref/** - - modules/cellranger/gtf/** - - tests/modules/cellranger/gtf/** + - modules/nf-core/cellranger/count/** + - tests/modules/nf-core/cellranger/count/** + - modules/nf-core/cellranger/mkref/** + - tests/modules/nf-core/cellranger/mkref/** + - modules/nf-core/cellranger/gtf/** + - tests/modules/nf-core/cellranger/gtf/** cellranger/gtf: - - modules/cellranger/gtf/** - - tests/modules/cellranger/gtf/** + - modules/nf-core/cellranger/gtf/** + - tests/modules/nf-core/cellranger/gtf/** cellranger/mkfastq: - - modules/cellranger/mkfastq/** - - tests/modules/cellranger/mkfastq/** + - modules/nf-core/cellranger/mkfastq/** + - tests/modules/nf-core/cellranger/mkfastq/** cellranger/mkgtf: - - modules/cellranger/mkgtf/** - - tests/modules/cellranger/mkgtf/** + - modules/nf-core/cellranger/mkgtf/** + - tests/modules/nf-core/cellranger/mkgtf/** cellranger/mkref: - - modules/cellranger/mkref/** - - tests/modules/cellranger/mkref/** - - modules/cellranger/gtf/** - - tests/modules/cellranger/gtf/** + - modules/nf-core/cellranger/mkref/** + - tests/modules/nf-core/cellranger/mkref/** + - modules/nf-core/cellranger/gtf/** + - tests/modules/nf-core/cellranger/gtf/** centrifuge/centrifuge: - - modules/centrifuge/centrifuge/** - - tests/modules/centrifuge/centrifuge/** + - modules/nf-core/centrifuge/centrifuge/** + - tests/modules/nf-core/centrifuge/centrifuge/** checkm/lineagewf: - - modules/checkm/lineagewf/** - - tests/modules/checkm/lineagewf/** + - modules/nf-core/checkm/lineagewf/** + - tests/modules/nf-core/checkm/lineagewf/** checkm/qa: - - modules/checkm/qa/** - - tests/modules/checkm/qa/** + - modules/nf-core/checkm/qa/** + - tests/modules/nf-core/checkm/qa/** chromap/chromap: - - modules/chromap/chromap/** - - tests/modules/chromap/chromap/** + - modules/nf-core/chromap/chromap/** + - tests/modules/nf-core/chromap/chromap/** chromap/index: - - modules/chromap/index/** - - tests/modules/chromap/index/** + - modules/nf-core/chromap/index/** + - tests/modules/nf-core/chromap/index/** clonalframeml: - - modules/clonalframeml/** - - tests/modules/clonalframeml/** + - modules/nf-core/clonalframeml/** + - tests/modules/nf-core/clonalframeml/** cmseq/polymut: - - modules/cmseq/polymut/** - - tests/modules/cmseq/polymut/** + - modules/nf-core/cmseq/polymut/** + - tests/modules/nf-core/cmseq/polymut/** cnvkit/antitarget: - - modules/cnvkit/antitarget/** - - tests/modules/cnvkit/antitarget/** + - modules/nf-core/cnvkit/antitarget/** + - tests/modules/nf-core/cnvkit/antitarget/** cnvkit/batch: - - modules/cnvkit/batch/** - - tests/modules/cnvkit/batch/** + - modules/nf-core/cnvkit/batch/** + - tests/modules/nf-core/cnvkit/batch/** cnvkit/reference: - - modules/cnvkit/reference/** - - tests/modules/cnvkit/reference/** + - modules/nf-core/cnvkit/reference/** + - tests/modules/nf-core/cnvkit/reference/** controlfreec/assesssignificance: - - modules/controlfreec/assesssignificance/** - - tests/modules/controlfreec/assesssignificance/** + - modules/nf-core/controlfreec/assesssignificance/** + - tests/modules/nf-core/controlfreec/assesssignificance/** controlfreec/freec: - - modules/controlfreec/freec/** - - tests/modules/controlfreec/freec/** + - modules/nf-core/controlfreec/freec/** + - tests/modules/nf-core/controlfreec/freec/** controlfreec/freec2bed: - - modules/controlfreec/freec2bed/** - - tests/modules/controlfreec/freec2bed/** + - modules/nf-core/controlfreec/freec2bed/** + - tests/modules/nf-core/controlfreec/freec2bed/** controlfreec/freec2circos: - - modules/controlfreec/freec2circos/** - - tests/modules/controlfreec/freec2circos/** + - modules/nf-core/controlfreec/freec2circos/** + - tests/modules/nf-core/controlfreec/freec2circos/** controlfreec/makegraph: - - modules/controlfreec/makegraph/** - - tests/modules/controlfreec/makegraph/** + - modules/nf-core/controlfreec/makegraph/** + - tests/modules/nf-core/controlfreec/makegraph/** cooler/cload: - - modules/cooler/cload/** - - tests/modules/cooler/cload/** + - modules/nf-core/cooler/cload/** + - tests/modules/nf-core/cooler/cload/** cooler/digest: - - modules/cooler/digest/** - - tests/modules/cooler/digest/** + - modules/nf-core/cooler/digest/** + - tests/modules/nf-core/cooler/digest/** cooler/dump: - - modules/cooler/dump/** - - tests/modules/cooler/dump/** + - modules/nf-core/cooler/dump/** + - tests/modules/nf-core/cooler/dump/** cooler/merge: - - modules/cooler/merge/** - - tests/modules/cooler/merge/** + - modules/nf-core/cooler/merge/** + - tests/modules/nf-core/cooler/merge/** cooler/zoomify: - - modules/cooler/zoomify/** + - modules/nf-core/cooler/zoomify/** - tests/software/cooler/zoomify/** csvtk/concat: - - modules/csvtk/concat/** - - tests/modules/csvtk/concat/** + - modules/nf-core/csvtk/concat/** + - tests/modules/nf-core/csvtk/concat/** csvtk/split: - - modules/csvtk/split/** - - tests/modules/csvtk/split/** + - modules/nf-core/csvtk/split/** + - tests/modules/nf-core/csvtk/split/** custom/dumpsoftwareversions: - - modules/custom/dumpsoftwareversions/** - - tests/modules/custom/dumpsoftwareversions/** + - modules/nf-core/custom/dumpsoftwareversions/** + - tests/modules/nf-core/custom/dumpsoftwareversions/** custom/getchromsizes: - - modules/custom/getchromsizes/** - - tests/modules/custom/getchromsizes/** + - modules/nf-core/custom/getchromsizes/** + - tests/modules/nf-core/custom/getchromsizes/** custom/sratoolsncbisettings: - - modules/custom/sratoolsncbisettings/** - - tests/modules/custom/sratoolsncbisettings/** + - modules/nf-core/custom/sratoolsncbisettings/** + - tests/modules/nf-core/custom/sratoolsncbisettings/** cutadapt: - - modules/cutadapt/** - - tests/modules/cutadapt/** + - modules/nf-core/cutadapt/** + - tests/modules/nf-core/cutadapt/** damageprofiler: - - modules/damageprofiler/** - - tests/modules/damageprofiler/** + - modules/nf-core/damageprofiler/** + - tests/modules/nf-core/damageprofiler/** dastool/dastool: - - modules/dastool/dastool/** - - tests/modules/dastool/dastool/** + - modules/nf-core/dastool/dastool/** + - tests/modules/nf-core/dastool/dastool/** dastool/fastatocontig2bin: - - modules/dastool/fastatocontig2bin/** - - tests/modules/dastool/fastatocontig2bin/** + - modules/nf-core/dastool/fastatocontig2bin/** + - tests/modules/nf-core/dastool/fastatocontig2bin/** dastool/scaffolds2bin: - - modules/dastool/scaffolds2bin/** - - tests/modules/dastool/scaffolds2bin/** + - modules/nf-core/dastool/scaffolds2bin/** + - tests/modules/nf-core/dastool/scaffolds2bin/** dedup: - - modules/dedup/** - - tests/modules/dedup/** + - modules/nf-core/dedup/** + - tests/modules/nf-core/dedup/** deeparg/downloaddata: - - modules/deeparg/downloaddata/** - - tests/modules/deeparg/downloaddata/** + - modules/nf-core/deeparg/downloaddata/** + - tests/modules/nf-core/deeparg/downloaddata/** deeparg/predict: - - modules/deeparg/predict/** - - tests/modules/deeparg/predict/** + - modules/nf-core/deeparg/predict/** + - tests/modules/nf-core/deeparg/predict/** deepbgc/download: - - modules/deepbgc/download/** - - tests/modules/deepbgc/download/** + - modules/nf-core/deepbgc/download/** + - tests/modules/nf-core/deepbgc/download/** deepbgc/pipeline: - - modules/deepbgc/pipeline/** - - tests/modules/deepbgc/pipeline/** + - modules/nf-core/deepbgc/pipeline/** + - tests/modules/nf-core/deepbgc/pipeline/** deeptools/bamcoverage: - - modules/deeptools/bamcoverage/** - - tests/modules/deeptools/bamcoverage/** + - modules/nf-core/deeptools/bamcoverage/** + - tests/modules/nf-core/deeptools/bamcoverage/** deeptools/computematrix: - - modules/deeptools/computematrix/** - - tests/modules/deeptools/computematrix/** + - modules/nf-core/deeptools/computematrix/** + - tests/modules/nf-core/deeptools/computematrix/** deeptools/plotfingerprint: - - modules/deeptools/plotfingerprint/** - - tests/modules/deeptools/plotfingerprint/** + - modules/nf-core/deeptools/plotfingerprint/** + - tests/modules/nf-core/deeptools/plotfingerprint/** deeptools/plotheatmap: - - modules/deeptools/plotheatmap/** - - tests/modules/deeptools/plotheatmap/** + - modules/nf-core/deeptools/plotheatmap/** + - tests/modules/nf-core/deeptools/plotheatmap/** deeptools/plotprofile: - - modules/deeptools/plotprofile/** - - tests/modules/deeptools/plotprofile/** + - modules/nf-core/deeptools/plotprofile/** + - tests/modules/nf-core/deeptools/plotprofile/** deepvariant: - - modules/deepvariant/** - - tests/modules/deepvariant/** + - modules/nf-core/deepvariant/** + - tests/modules/nf-core/deepvariant/** delly/call: - - modules/delly/call/** - - tests/modules/delly/call/** + - modules/nf-core/delly/call/** + - tests/modules/nf-core/delly/call/** diamond/blastp: - - modules/diamond/blastp/** - - tests/modules/diamond/blastp/** + - modules/nf-core/diamond/blastp/** + - tests/modules/nf-core/diamond/blastp/** diamond/blastx: - - modules/diamond/blastx/** - - tests/modules/diamond/blastx/** + - modules/nf-core/diamond/blastx/** + - tests/modules/nf-core/diamond/blastx/** diamond/makedb: - - modules/diamond/makedb/** - - tests/modules/diamond/makedb/** + - modules/nf-core/diamond/makedb/** + - tests/modules/nf-core/diamond/makedb/** dragmap/align: - - modules/dragmap/align/** - - tests/modules/dragmap/align/** + - modules/nf-core/dragmap/align/** + - tests/modules/nf-core/dragmap/align/** dragmap/hashtable: - - modules/dragmap/hashtable/** - - tests/modules/dragmap/hashtable/** + - modules/nf-core/dragmap/hashtable/** + - tests/modules/nf-core/dragmap/hashtable/** dragonflye: - - modules/dragonflye/** - - tests/modules/dragonflye/** + - modules/nf-core/dragonflye/** + - tests/modules/nf-core/dragonflye/** dshbio/exportsegments: - - modules/dshbio/exportsegments/** - - tests/modules/dshbio/exportsegments/** + - modules/nf-core/dshbio/exportsegments/** + - tests/modules/nf-core/dshbio/exportsegments/** dshbio/filterbed: - - modules/dshbio/filterbed/** - - tests/modules/dshbio/filterbed/** + - modules/nf-core/dshbio/filterbed/** + - tests/modules/nf-core/dshbio/filterbed/** dshbio/filtergff3: - - modules/dshbio/filtergff3/** - - tests/modules/dshbio/filtergff3/** + - modules/nf-core/dshbio/filtergff3/** + - tests/modules/nf-core/dshbio/filtergff3/** dshbio/splitbed: - - modules/dshbio/splitbed/** - - tests/modules/dshbio/splitbed/** + - modules/nf-core/dshbio/splitbed/** + - tests/modules/nf-core/dshbio/splitbed/** dshbio/splitgff3: - - modules/dshbio/splitgff3/** - - tests/modules/dshbio/splitgff3/** + - modules/nf-core/dshbio/splitgff3/** + - tests/modules/nf-core/dshbio/splitgff3/** ectyper: - - modules/ectyper/** - - tests/modules/ectyper/** + - modules/nf-core/ectyper/** + - tests/modules/nf-core/ectyper/** eido/convert: - - modules/eido/convert/** - - tests/modules/eido/convert/** + - modules/nf-core/eido/convert/** + - tests/modules/nf-core/eido/convert/** eido/validate: - - modules/eido/validate/** - - tests/modules/eido/validate/** + - modules/nf-core/eido/validate/** + - tests/modules/nf-core/eido/validate/** elprep/filter: - - modules/elprep/filter/** - - tests/modules/elprep/filter/** + - modules/nf-core/elprep/filter/** + - tests/modules/nf-core/elprep/filter/** elprep/merge: - - modules/elprep/merge/** - - tests/modules/elprep/merge/** + - modules/nf-core/elprep/merge/** + - tests/modules/nf-core/elprep/merge/** elprep/split: - - modules/elprep/split/** - - tests/modules/elprep/split/** + - modules/nf-core/elprep/split/** + - tests/modules/nf-core/elprep/split/** emboss/seqret: - - modules/emboss/seqret/** - - tests/modules/emboss/seqret/** + - modules/nf-core/emboss/seqret/** + - tests/modules/nf-core/emboss/seqret/** emmtyper: - - modules/emmtyper/** - - tests/modules/emmtyper/** + - modules/nf-core/emmtyper/** + - tests/modules/nf-core/emmtyper/** endorspy: - - modules/endorspy/** - - tests/modules/endorspy/** + - modules/nf-core/endorspy/** + - tests/modules/nf-core/endorspy/** ensemblvep: - - modules/ensemblvep/** - - tests/modules/ensemblvep/** + - modules/nf-core/ensemblvep/** + - tests/modules/nf-core/ensemblvep/** entrezdirect/esearch: - - modules/entrezdirect/esearch/** - - tests/modules/entrezdirect/esearch/** + - modules/nf-core/entrezdirect/esearch/** + - tests/modules/nf-core/entrezdirect/esearch/** entrezdirect/esummary: - - modules/entrezdirect/esummary/** - - tests/modules/entrezdirect/esummary/** + - modules/nf-core/entrezdirect/esummary/** + - tests/modules/nf-core/entrezdirect/esummary/** entrezdirect/xtract: - - modules/entrezdirect/xtract/** - - tests/modules/entrezdirect/xtract/** + - modules/nf-core/entrezdirect/xtract/** + - tests/modules/nf-core/entrezdirect/xtract/** epang: - - modules/epang/** - - tests/modules/epang/ + - modules/nf-core/epang/** + - tests/modules/nf-core/epang/ expansionhunter: - - modules/expansionhunter/** - - tests/modules/expansionhunter/** + - modules/nf-core/expansionhunter/** + - tests/modules/nf-core/expansionhunter/** faqcs: - - modules/faqcs/** - - tests/modules/faqcs/** + - modules/nf-core/faqcs/** + - tests/modules/nf-core/faqcs/** fargene: - - modules/fargene/** - - tests/modules/fargene/** + - modules/nf-core/fargene/** + - tests/modules/nf-core/fargene/** fastani: - - modules/fastani/** - - tests/modules/fastani/** + - modules/nf-core/fastani/** + - tests/modules/nf-core/fastani/** fastawindows: - - modules/fastawindows/** - - tests/modules/fastawindows/** + - modules/nf-core/fastawindows/** + - tests/modules/nf-core/fastawindows/** fastk/fastk: - - modules/fastk/fastk/** - - tests/modules/fastk/fastk/** + - modules/nf-core/fastk/fastk/** + - tests/modules/nf-core/fastk/fastk/** fastk/histex: - - modules/fastk/histex/** - - tests/modules/fastk/histex/** + - modules/nf-core/fastk/histex/** + - tests/modules/nf-core/fastk/histex/** fastk/merge: - - modules/fastk/merge/** - - tests/modules/fastk/merge/** + - modules/nf-core/fastk/merge/** + - tests/modules/nf-core/fastk/merge/** fastp: - - modules/fastp/** - - tests/modules/fastp/** + - modules/nf-core/fastp/** + - tests/modules/nf-core/fastp/** fastqc: - - modules/fastqc/** - - tests/modules/fastqc/** + - modules/nf-core/fastqc/** + - tests/modules/nf-core/fastqc/** fastqscan: - - modules/fastqscan/** - - tests/modules/fastqscan/** + - modules/nf-core/fastqscan/** + - tests/modules/nf-core/fastqscan/** fasttree: - - modules/fasttree/** - - tests/modules/fasttree/** + - modules/nf-core/fasttree/** + - tests/modules/nf-core/fasttree/** fcs/fcsadaptor: - - modules/fcs/fcsadaptor/** - - tests/modules/fcs/fcsadaptor/** + - modules/nf-core/fcs/fcsadaptor/** + - tests/modules/nf-core/fcs/fcsadaptor/** ffq: - - modules/ffq/** - - tests/modules/ffq/** + - modules/nf-core/ffq/** + - tests/modules/nf-core/ffq/** fgbio/callmolecularconsensusreads: - - modules/fgbio/callmolecularconsensusreads/** - - tests/modules/fgbio/callmolecularconsensusreads/** + - modules/nf-core/fgbio/callmolecularconsensusreads/** + - tests/modules/nf-core/fgbio/callmolecularconsensusreads/** fgbio/fastqtobam: - - modules/fgbio/fastqtobam/** - - tests/modules/fgbio/fastqtobam/** + - modules/nf-core/fgbio/fastqtobam/** + - tests/modules/nf-core/fgbio/fastqtobam/** fgbio/groupreadsbyumi: - - modules/fgbio/groupreadsbyumi/** - - tests/modules/fgbio/groupreadsbyumi/** + - modules/nf-core/fgbio/groupreadsbyumi/** + - tests/modules/nf-core/fgbio/groupreadsbyumi/** fgbio/sortbam: - - modules/fgbio/sortbam/** - - tests/modules/fgbio/sortbam/** + - modules/nf-core/fgbio/sortbam/** + - tests/modules/nf-core/fgbio/sortbam/** filtlong: - - modules/filtlong/** - - tests/modules/filtlong/** + - modules/nf-core/filtlong/** + - tests/modules/nf-core/filtlong/** flash: - - modules/flash/** - - tests/modules/flash/** + - modules/nf-core/flash/** + - tests/modules/nf-core/flash/** flye: - - modules/flye/** - - tests/modules/flye/** + - modules/nf-core/flye/** + - tests/modules/nf-core/flye/** fq/lint: - - modules/fq/lint/** - - tests/modules/fq/lint/** + - modules/nf-core/fq/lint/** + - tests/modules/nf-core/fq/lint/** freebayes: - - modules/freebayes/** - - tests/modules/freebayes/** + - modules/nf-core/freebayes/** + - tests/modules/nf-core/freebayes/** gamma/gamma: - - modules/gamma/gamma/** - - tests/modules/gamma/gamma/** + - modules/nf-core/gamma/gamma/** + - tests/modules/nf-core/gamma/gamma/** gappa/examineassign: - - modules/gappa/examineassign/** - - tests/modules/gappa/examineassign/** + - modules/nf-core/gappa/examineassign/** + - tests/modules/nf-core/gappa/examineassign/** gappa/examinegraft: - - modules/gappa/examinegraft/** - - tests/modules/gappa/examinegraft/** + - modules/nf-core/gappa/examinegraft/** + - tests/modules/nf-core/gappa/examinegraft/** gappa/examineheattree: - - modules/gappa/examineheattree/** - - tests/modules/gappa/examineheattree/** + - modules/nf-core/gappa/examineheattree/** + - tests/modules/nf-core/gappa/examineheattree/** gatk/indelrealigner: - - modules/gatk/indelrealigner/** - - tests/modules/gatk/indelrealigner/** + - modules/nf-core/gatk/indelrealigner/** + - tests/modules/nf-core/gatk/indelrealigner/** gatk/realignertargetcreator: - - modules/gatk/realignertargetcreator/** - - tests/modules/gatk/realignertargetcreator/** + - modules/nf-core/gatk/realignertargetcreator/** + - tests/modules/nf-core/gatk/realignertargetcreator/** gatk/unifiedgenotyper: - - modules/gatk/unifiedgenotyper/** - - tests/modules/gatk/unifiedgenotyper/** + - modules/nf-core/gatk/unifiedgenotyper/** + - tests/modules/nf-core/gatk/unifiedgenotyper/** gatk4/applybqsr: - - modules/gatk4/applybqsr/** - - tests/modules/gatk4/applybqsr/** + - modules/nf-core/gatk4/applybqsr/** + - tests/modules/nf-core/gatk4/applybqsr/** gatk4/applybqsrspark: - - modules/gatk4/applybqsrspark/** - - tests/modules/gatk4/applybqsrspark/** + - modules/nf-core/gatk4/applybqsrspark/** + - tests/modules/nf-core/gatk4/applybqsrspark/** gatk4/applyvqsr: - - modules/gatk4/applyvqsr/** - - tests/modules/gatk4/applyvqsr/** + - modules/nf-core/gatk4/applyvqsr/** + - tests/modules/nf-core/gatk4/applyvqsr/** gatk4/baserecalibrator: - - modules/gatk4/baserecalibrator/** - - tests/modules/gatk4/baserecalibrator/** + - modules/nf-core/gatk4/baserecalibrator/** + - tests/modules/nf-core/gatk4/baserecalibrator/** gatk4/baserecalibratorspark: - - modules/gatk4/baserecalibratorspark/** - - tests/modules/gatk4/baserecalibratorspark/** + - modules/nf-core/gatk4/baserecalibratorspark/** + - tests/modules/nf-core/gatk4/baserecalibratorspark/** gatk4/bedtointervallist: - - modules/gatk4/bedtointervallist/** - - tests/modules/gatk4/bedtointervallist/** + - modules/nf-core/gatk4/bedtointervallist/** + - tests/modules/nf-core/gatk4/bedtointervallist/** gatk4/calculatecontamination: - - modules/gatk4/calculatecontamination/** - - tests/modules/gatk4/calculatecontamination/** + - modules/nf-core/gatk4/calculatecontamination/** + - tests/modules/nf-core/gatk4/calculatecontamination/** gatk4/calibratedragstrmodel: - - modules/gatk4/calibratedragstrmodel/** - - tests/modules/gatk4/calibratedragstrmodel/** + - modules/nf-core/gatk4/calibratedragstrmodel/** + - tests/modules/nf-core/gatk4/calibratedragstrmodel/** gatk4/cnnscorevariants: - - modules/gatk4/cnnscorevariants/** - - tests/modules/gatk4/cnnscorevariants/** + - modules/nf-core/gatk4/cnnscorevariants/** + - tests/modules/nf-core/gatk4/cnnscorevariants/** gatk4/collectreadcounts: - - modules/gatk4/collectreadcounts/** - - tests/modules/gatk4/collectreadcounts/** + - modules/nf-core/gatk4/collectreadcounts/** + - tests/modules/nf-core/gatk4/collectreadcounts/** gatk4/collectsvevidence: - - modules/gatk4/collectsvevidence/** - - tests/modules/gatk4/collectsvevidence/** + - modules/nf-core/gatk4/collectsvevidence/** + - tests/modules/nf-core/gatk4/collectsvevidence/** gatk4/combinegvcfs: - - modules/gatk4/combinegvcfs/** - - tests/modules/gatk4/combinegvcfs/** + - modules/nf-core/gatk4/combinegvcfs/** + - tests/modules/nf-core/gatk4/combinegvcfs/** gatk4/composestrtablefile: - - modules/gatk4/composestrtablefile/** - - tests/modules/gatk4/composestrtablefile/** + - modules/nf-core/gatk4/composestrtablefile/** + - tests/modules/nf-core/gatk4/composestrtablefile/** gatk4/createsequencedictionary: - - modules/gatk4/createsequencedictionary/** - - tests/modules/gatk4/createsequencedictionary/** + - modules/nf-core/gatk4/createsequencedictionary/** + - tests/modules/nf-core/gatk4/createsequencedictionary/** gatk4/createsomaticpanelofnormals: - - modules/gatk4/createsomaticpanelofnormals/** - - tests/modules/gatk4/createsomaticpanelofnormals/** + - modules/nf-core/gatk4/createsomaticpanelofnormals/** + - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/** gatk4/estimatelibrarycomplexity: - - modules/gatk4/estimatelibrarycomplexity/** - - tests/modules/gatk4/estimatelibrarycomplexity/** + - modules/nf-core/gatk4/estimatelibrarycomplexity/** + - tests/modules/nf-core/gatk4/estimatelibrarycomplexity/** gatk4/fastqtosam: - - modules/gatk4/fastqtosam/** - - tests/modules/gatk4/fastqtosam/** + - modules/nf-core/gatk4/fastqtosam/** + - tests/modules/nf-core/gatk4/fastqtosam/** gatk4/filtermutectcalls: - - modules/gatk4/filtermutectcalls/** - - tests/modules/gatk4/filtermutectcalls/** + - modules/nf-core/gatk4/filtermutectcalls/** + - tests/modules/nf-core/gatk4/filtermutectcalls/** gatk4/filtervarianttranches: - - modules/gatk4/filtervarianttranches/** - - tests/modules/gatk4/filtervarianttranches/** + - modules/nf-core/gatk4/filtervarianttranches/** + - tests/modules/nf-core/gatk4/filtervarianttranches/** gatk4/gatherbqsrreports: - - modules/gatk4/gatherbqsrreports/** - - tests/modules/gatk4/gatherbqsrreports/** + - modules/nf-core/gatk4/gatherbqsrreports/** + - tests/modules/nf-core/gatk4/gatherbqsrreports/** gatk4/gatherpileupsummaries: - - modules/gatk4/gatherpileupsummaries/** - - tests/modules/gatk4/gatherpileupsummaries/** + - modules/nf-core/gatk4/gatherpileupsummaries/** + - tests/modules/nf-core/gatk4/gatherpileupsummaries/** gatk4/genomicsdbimport: - - modules/gatk4/genomicsdbimport/** - - tests/modules/gatk4/genomicsdbimport/** + - modules/nf-core/gatk4/genomicsdbimport/** + - tests/modules/nf-core/gatk4/genomicsdbimport/** gatk4/genotypegvcfs: - - modules/gatk4/genotypegvcfs/** - - tests/modules/gatk4/genotypegvcfs/** + - modules/nf-core/gatk4/genotypegvcfs/** + - tests/modules/nf-core/gatk4/genotypegvcfs/** gatk4/getpileupsummaries: - - modules/gatk4/getpileupsummaries/** - - tests/modules/gatk4/getpileupsummaries/** + - modules/nf-core/gatk4/getpileupsummaries/** + - tests/modules/nf-core/gatk4/getpileupsummaries/** gatk4/haplotypecaller: - - modules/gatk4/haplotypecaller/** - - tests/modules/gatk4/haplotypecaller/** + - modules/nf-core/gatk4/haplotypecaller/** + - tests/modules/nf-core/gatk4/haplotypecaller/** gatk4/indexfeaturefile: - - modules/gatk4/indexfeaturefile/** - - tests/modules/gatk4/indexfeaturefile/** + - modules/nf-core/gatk4/indexfeaturefile/** + - tests/modules/nf-core/gatk4/indexfeaturefile/** gatk4/intervallisttobed: - - modules/gatk4/intervallisttobed/** - - tests/modules/gatk4/intervallisttobed/** + - modules/nf-core/gatk4/intervallisttobed/** + - tests/modules/nf-core/gatk4/intervallisttobed/** gatk4/intervallisttools: - - modules/gatk4/intervallisttools/** - - tests/modules/gatk4/intervallisttools/** + - modules/nf-core/gatk4/intervallisttools/** + - tests/modules/nf-core/gatk4/intervallisttools/** gatk4/learnreadorientationmodel: - - modules/gatk4/learnreadorientationmodel/** - - tests/modules/gatk4/learnreadorientationmodel/** + - modules/nf-core/gatk4/learnreadorientationmodel/** + - tests/modules/nf-core/gatk4/learnreadorientationmodel/** gatk4/leftalignandtrimvariants: - - modules/gatk4/leftalignandtrimvariants/** - - tests/modules/gatk4/leftalignandtrimvariants/** + - modules/nf-core/gatk4/leftalignandtrimvariants/** + - tests/modules/nf-core/gatk4/leftalignandtrimvariants/** gatk4/markduplicates: - - modules/gatk4/markduplicates/** - - tests/modules/gatk4/markduplicates/** + - modules/nf-core/gatk4/markduplicates/** + - tests/modules/nf-core/gatk4/markduplicates/** gatk4/markduplicatesspark: - - modules/gatk4/markduplicatesspark/** - - tests/modules/gatk4/markduplicatesspark/** + - modules/nf-core/gatk4/markduplicatesspark/** + - tests/modules/nf-core/gatk4/markduplicatesspark/** gatk4/mergebamalignment: - - modules/gatk4/mergebamalignment/** - - tests/modules/gatk4/mergebamalignment/** + - modules/nf-core/gatk4/mergebamalignment/** + - tests/modules/nf-core/gatk4/mergebamalignment/** gatk4/mergemutectstats: - - modules/gatk4/mergemutectstats/** - - tests/modules/gatk4/mergemutectstats/** + - modules/nf-core/gatk4/mergemutectstats/** + - tests/modules/nf-core/gatk4/mergemutectstats/** gatk4/mergevcfs: - - modules/gatk4/mergevcfs/** - - tests/modules/gatk4/mergevcfs/** + - modules/nf-core/gatk4/mergevcfs/** + - tests/modules/nf-core/gatk4/mergevcfs/** gatk4/mutect2: - - modules/gatk4/mutect2/** - - tests/modules/gatk4/mutect2/** + - modules/nf-core/gatk4/mutect2/** + - tests/modules/nf-core/gatk4/mutect2/** gatk4/printsvevidence: - - modules/gatk4/printsvevidence/** - - tests/modules/gatk4/printsvevidence/** + - modules/nf-core/gatk4/printsvevidence/** + - tests/modules/nf-core/gatk4/printsvevidence/** gatk4/reblockgvcf: - - modules/gatk4/reblockgvcf/** - - tests/modules/gatk4/reblockgvcf/** + - modules/nf-core/gatk4/reblockgvcf/** + - tests/modules/nf-core/gatk4/reblockgvcf/** gatk4/revertsam: - - modules/gatk4/revertsam/** - - tests/modules/gatk4/revertsam/** + - modules/nf-core/gatk4/revertsam/** + - tests/modules/nf-core/gatk4/revertsam/** gatk4/samtofastq: - - modules/gatk4/samtofastq/** - - tests/modules/gatk4/samtofastq/** + - modules/nf-core/gatk4/samtofastq/** + - tests/modules/nf-core/gatk4/samtofastq/** gatk4/selectvariants: - - modules/gatk4/selectvariants/** - - tests/modules/gatk4/selectvariants/** + - modules/nf-core/gatk4/selectvariants/** + - tests/modules/nf-core/gatk4/selectvariants/** gatk4/splitintervals: - - modules/gatk4/splitintervals/** - - tests/modules/gatk4/splitintervals/** + - modules/nf-core/gatk4/splitintervals/** + - tests/modules/nf-core/gatk4/splitintervals/** gatk4/splitncigarreads: - - modules/gatk4/splitncigarreads/** - - tests/modules/gatk4/splitncigarreads/** + - modules/nf-core/gatk4/splitncigarreads/** + - tests/modules/nf-core/gatk4/splitncigarreads/** gatk4/variantfiltration: - - modules/gatk4/variantfiltration/** - - tests/modules/gatk4/variantfiltration/** + - modules/nf-core/gatk4/variantfiltration/** + - tests/modules/nf-core/gatk4/variantfiltration/** gatk4/variantrecalibrator: - - modules/gatk4/variantrecalibrator/** - - tests/modules/gatk4/variantrecalibrator/** + - modules/nf-core/gatk4/variantrecalibrator/** + - tests/modules/nf-core/gatk4/variantrecalibrator/** gecco/run: - - modules/gecco/run/** - - tests/modules/gecco/run/** + - modules/nf-core/gecco/run/** + - tests/modules/nf-core/gecco/run/** genescopefk: - - modules/genescopefk/** - - tests/modules/genescopefk/** + - modules/nf-core/genescopefk/** + - tests/modules/nf-core/genescopefk/** genmap/index: - - modules/genmap/index/** - - tests/modules/genmap/index/** + - modules/nf-core/genmap/index/** + - tests/modules/nf-core/genmap/index/** genmap/mappability: - - modules/genmap/mappability/** - - tests/modules/genmap/mappability/** + - modules/nf-core/genmap/mappability/** + - tests/modules/nf-core/genmap/mappability/** genmod/annotate: - - modules/genmod/annotate/** - - tests/modules/genmod/annotate/** + - modules/nf-core/genmod/annotate/** + - tests/modules/nf-core/genmod/annotate/** genmod/compound: - - modules/genmod/compound/** - - tests/modules/genmod/compound/** + - modules/nf-core/genmod/compound/** + - tests/modules/nf-core/genmod/compound/** genmod/models: - - modules/genmod/models/** - - tests/modules/genmod/models/** + - modules/nf-core/genmod/models/** + - tests/modules/nf-core/genmod/models/** genmod/score: - - modules/genmod/score/** - - tests/modules/genmod/score/** + - modules/nf-core/genmod/score/** + - tests/modules/nf-core/genmod/score/** genomescope2: - - modules/genomescope2/** - - tests/modules/genomescope2/** + - modules/nf-core/genomescope2/** + - tests/modules/nf-core/genomescope2/** genotyphi/parse: - - modules/genotyphi/parse/** - - tests/modules/genotyphi/parse/** + - modules/nf-core/genotyphi/parse/** + - tests/modules/nf-core/genotyphi/parse/** genrich: - - modules/genrich/** - - tests/modules/genrich/** + - modules/nf-core/genrich/** + - tests/modules/nf-core/genrich/** gfaffix: - - modules/gfaffix/** - - tests/modules/gfaffix/** + - modules/nf-core/gfaffix/** + - tests/modules/nf-core/gfaffix/** gffread: - - modules/gffread/** - - tests/modules/gffread/** + - modules/nf-core/gffread/** + - tests/modules/nf-core/gffread/** glimpse/chunk: - - modules/glimpse/chunk/** - - tests/modules/glimpse/chunk/** + - modules/nf-core/glimpse/chunk/** + - tests/modules/nf-core/glimpse/chunk/** glnexus: - - modules/glnexus/** - - tests/modules/glnexus/** + - modules/nf-core/glnexus/** + - tests/modules/nf-core/glnexus/** goat/taxonsearch: - - modules/goat/taxonsearch/** - - tests/modules/goat/taxonsearch/** + - modules/nf-core/goat/taxonsearch/** + - tests/modules/nf-core/goat/taxonsearch/** graphmap2/align: - - modules/graphmap2/align/** - - tests/modules/graphmap2/align/** + - modules/nf-core/graphmap2/align/** + - tests/modules/nf-core/graphmap2/align/** graphmap2/index: - - modules/graphmap2/index/** - - tests/modules/graphmap2/index/** + - modules/nf-core/graphmap2/index/** + - tests/modules/nf-core/graphmap2/index/** gstama/collapse: - - modules/gstama/collapse/** - - tests/modules/gstama/collapse/** + - modules/nf-core/gstama/collapse/** + - tests/modules/nf-core/gstama/collapse/** gstama/merge: - - modules/gstama/merge/** - - tests/modules/gstama/merge/** + - modules/nf-core/gstama/merge/** + - tests/modules/nf-core/gstama/merge/** gstama/polyacleanup: - - modules/gstama/polyacleanup/** - - tests/modules/gstama/polyacleanup/** + - modules/nf-core/gstama/polyacleanup/** + - tests/modules/nf-core/gstama/polyacleanup/** gtdbtk/classifywf: - - modules/gtdbtk/classifywf/** - - tests/modules/gtdbtk/classifywf/** + - modules/nf-core/gtdbtk/classifywf/** + - tests/modules/nf-core/gtdbtk/classifywf/** gubbins: - - modules/gubbins/** - - tests/modules/gubbins/** + - modules/nf-core/gubbins/** + - tests/modules/nf-core/gubbins/** gunc/downloaddb: - - modules/gunc/downloaddb/** - - tests/modules/gunc/downloaddb/** + - modules/nf-core/gunc/downloaddb/** + - tests/modules/nf-core/gunc/downloaddb/** gunc/run: - - modules/gunc/run/** - - tests/modules/gunc/run/** + - modules/nf-core/gunc/run/** + - tests/modules/nf-core/gunc/run/** gunzip: - - modules/gunzip/** - - tests/modules/gunzip/** + - modules/nf-core/gunzip/** + - tests/modules/nf-core/gunzip/** gvcftools/extractvariants: - - modules/gvcftools/extractvariants/** - - tests/modules/gvcftools/extractvariants/** + - modules/nf-core/gvcftools/extractvariants/** + - tests/modules/nf-core/gvcftools/extractvariants/** hamronization/abricate: - - modules/hamronization/abricate/** - - tests/modules/hamronization/abricate/** + - modules/nf-core/hamronization/abricate/** + - tests/modules/nf-core/hamronization/abricate/** hamronization/amrfinderplus: - - modules/hamronization/amrfinderplus/** - - tests/modules/hamronization/amrfinderplus/** + - modules/nf-core/hamronization/amrfinderplus/** + - tests/modules/nf-core/hamronization/amrfinderplus/** hamronization/deeparg: - - modules/hamronization/deeparg/** - - tests/modules/hamronization/deeparg/** + - modules/nf-core/hamronization/deeparg/** + - tests/modules/nf-core/hamronization/deeparg/** hamronization/fargene: - - modules/hamronization/fargene/** - - tests/modules/hamronization/fargene/** + - modules/nf-core/hamronization/fargene/** + - tests/modules/nf-core/hamronization/fargene/** hamronization/rgi: - - modules/hamronization/rgi/** - - tests/modules/hamronization/rgi/** + - modules/nf-core/hamronization/rgi/** + - tests/modules/nf-core/hamronization/rgi/** hamronization/summarize: - - modules/hamronization/summarize/** - - tests/modules/hamronization/summarize/** + - modules/nf-core/hamronization/summarize/** + - tests/modules/nf-core/hamronization/summarize/** haplocheck: - - modules/haplocheck/** - - tests/modules/haplocheck/** + - modules/nf-core/haplocheck/** + - tests/modules/nf-core/haplocheck/** haplogrep2/classify: - - modules/haplogrep2/classify/** - - tests/modules/haplogrep2/classify/** + - modules/nf-core/haplogrep2/classify/** + - tests/modules/nf-core/haplogrep2/classify/** happy/happy: - - modules/happy/happy/** - - tests/modules/happy/happy/** + - modules/nf-core/happy/happy/** + - tests/modules/nf-core/happy/happy/** happy/prepy: - - modules/happy/prepy/** - - tests/modules/happy/prepy/** + - modules/nf-core/happy/prepy/** + - tests/modules/nf-core/happy/prepy/** hicap: - - modules/hicap/** - - tests/modules/hicap/** + - modules/nf-core/hicap/** + - tests/modules/nf-core/hicap/** hifiasm: - - modules/hifiasm/** - - tests/modules/hifiasm/** + - modules/nf-core/hifiasm/** + - tests/modules/nf-core/hifiasm/** hisat2/align: - - modules/hisat2/align/** - - modules/hisat2/build/** - - modules/hisat2/extractsplicesites/** - - tests/modules/hisat2/align/** + - modules/nf-core/hisat2/align/** + - modules/nf-core/hisat2/build/** + - modules/nf-core/hisat2/extractsplicesites/** + - tests/modules/nf-core/hisat2/align/** hisat2/build: - - modules/hisat2/build/** - - modules/hisat2/extractsplicesites/** - - tests/modules/hisat2/build_test/** + - modules/nf-core/hisat2/build/** + - modules/nf-core/hisat2/extractsplicesites/** + - tests/modules/nf-core/hisat2/build_test/** hisat2/extractsplicesites: - - modules/hisat2/extractsplicesites/** - - tests/modules/hisat2/extractsplicesites/** + - modules/nf-core/hisat2/extractsplicesites/** + - tests/modules/nf-core/hisat2/extractsplicesites/** hmmcopy/gccounter: - - modules/hmmcopy/gccounter/** - - tests/modules/hmmcopy/gccounter/** + - modules/nf-core/hmmcopy/gccounter/** + - tests/modules/nf-core/hmmcopy/gccounter/** hmmcopy/generatemap: - - modules/hmmcopy/generatemap/** - - tests/modules/hmmcopy/generatemap/** + - modules/nf-core/hmmcopy/generatemap/** + - tests/modules/nf-core/hmmcopy/generatemap/** hmmcopy/mapcounter: - - modules/hmmcopy/mapcounter/** - - tests/modules/hmmcopy/mapcounter/** + - modules/nf-core/hmmcopy/mapcounter/** + - tests/modules/nf-core/hmmcopy/mapcounter/** hmmcopy/readcounter: - - modules/hmmcopy/readcounter/** - - tests/modules/hmmcopy/readcounter/** + - modules/nf-core/hmmcopy/readcounter/** + - tests/modules/nf-core/hmmcopy/readcounter/** hmmer/eslalimask: - - modules/hmmer/eslalimask/** - - tests/modules/hmmer/eslalimask/** + - modules/nf-core/hmmer/eslalimask/** + - tests/modules/nf-core/hmmer/eslalimask/** hmmer/eslreformat: - - modules/hmmer/eslreformat/** - - tests/modules/hmmer/eslreformat/** + - modules/nf-core/hmmer/eslreformat/** + - tests/modules/nf-core/hmmer/eslreformat/** hmmer/hmmalign: - - modules/hmmer/hmmalign/** - - tests/modules/hmmer/hmmalign/** + - modules/nf-core/hmmer/hmmalign/** + - tests/modules/nf-core/hmmer/hmmalign/** hmmer/hmmbuild: - - modules/hmmer/hmmbuild/** - - tests/modules/hmmer/hmmbuild/** + - modules/nf-core/hmmer/hmmbuild/** + - tests/modules/nf-core/hmmer/hmmbuild/** hmmer/hmmsearch: - - modules/hmmer/hmmsearch/** - - tests/modules/hmmer/hmmsearch/** + - modules/nf-core/hmmer/hmmsearch/** + - tests/modules/nf-core/hmmer/hmmsearch/** hmtnote: - - modules/hmtnote/** - - tests/modules/hmtnote/** + - modules/nf-core/hmtnote/** + - tests/modules/nf-core/hmtnote/** homer/annotatepeaks: - - modules/homer/annotatepeaks/** - - tests/modules/homer/annotatepeaks/** + - modules/nf-core/homer/annotatepeaks/** + - tests/modules/nf-core/homer/annotatepeaks/** homer/findpeaks: - - modules/homer/findpeaks/** - - modules/homer/maketagdirectory/** - - tests/modules/homer/findpeaks/** + - modules/nf-core/homer/findpeaks/** + - modules/nf-core/homer/maketagdirectory/** + - tests/modules/nf-core/homer/findpeaks/** homer/maketagdirectory: - - modules/homer/maketagdirectory/** - - tests/modules/homer/maketagdirectory/** + - modules/nf-core/homer/maketagdirectory/** + - tests/modules/nf-core/homer/maketagdirectory/** homer/makeucscfile: - - modules/homer/makeucscfile/** - - tests/modules/homer/makeucscfile/** + - modules/nf-core/homer/makeucscfile/** + - tests/modules/nf-core/homer/makeucscfile/** homer/pos2bed: - - modules/homer/pos2bed/** - - modules/homer/maketagdirectory/** - - modules/homer/findpeaks/** - - tests/modules/homer/pos2bed/** + - modules/nf-core/homer/pos2bed/** + - modules/nf-core/homer/maketagdirectory/** + - modules/nf-core/homer/findpeaks/** + - tests/modules/nf-core/homer/pos2bed/** hpsuissero: - - modules/hpsuissero/** - - tests/modules/hpsuissero/** + - modules/nf-core/hpsuissero/** + - tests/modules/nf-core/hpsuissero/** ichorcna/createpon: - - modules/ichorcna/createpon/** - - tests/modules/ichorcna/createpon/** + - modules/nf-core/ichorcna/createpon/** + - tests/modules/nf-core/ichorcna/createpon/** ichorcna/run: - - modules/ichorcna/run/** - - tests/modules/ichorcna/run/** + - modules/nf-core/ichorcna/run/** + - tests/modules/nf-core/ichorcna/run/** idr: - - modules/idr/** - - tests/modules/idr/** + - modules/nf-core/idr/** + - tests/modules/nf-core/idr/** imputeme/vcftoprs: - - modules/imputeme/vcftoprs/** - - tests/modules/imputeme/vcftoprs/** + - modules/nf-core/imputeme/vcftoprs/** + - tests/modules/nf-core/imputeme/vcftoprs/** instrain/profile: - - modules/instrain/profile/** - - tests/modules/instrain/profile/** + - modules/nf-core/instrain/profile/** + - tests/modules/nf-core/instrain/profile/** iqtree: - - modules/iqtree/** - - tests/modules/iqtree/** + - modules/nf-core/iqtree/** + - tests/modules/nf-core/iqtree/** ismapper: - - modules/ismapper/** - - tests/modules/ismapper/** + - modules/nf-core/ismapper/** + - tests/modules/nf-core/ismapper/** isoseq3/cluster: - - modules/isoseq3/cluster/** - - tests/modules/isoseq3/cluster/** + - modules/nf-core/isoseq3/cluster/** + - tests/modules/nf-core/isoseq3/cluster/** isoseq3/refine: - - modules/isoseq3/refine/** - - tests/modules/isoseq3/refine/** + - modules/nf-core/isoseq3/refine/** + - tests/modules/nf-core/isoseq3/refine/** ivar/consensus: - - modules/ivar/consensus/** - - tests/modules/ivar/consensus/** + - modules/nf-core/ivar/consensus/** + - tests/modules/nf-core/ivar/consensus/** ivar/trim: - - modules/ivar/trim/** - - tests/modules/ivar/trim/** + - modules/nf-core/ivar/trim/** + - tests/modules/nf-core/ivar/trim/** ivar/variants: - - modules/ivar/variants/** - - tests/modules/ivar/variants/** + - modules/nf-core/ivar/variants/** + - tests/modules/nf-core/ivar/variants/** jupyternotebook: - - modules/jupyternotebook/** - - tests/modules/jupyternotebook/** + - modules/nf-core/jupyternotebook/** + - tests/modules/nf-core/jupyternotebook/** kaiju/kaiju: - - modules/kaiju/kaiju/** - - tests/modules/kaiju/kaiju/** + - modules/nf-core/kaiju/kaiju/** + - tests/modules/nf-core/kaiju/kaiju/** kaiju/kaiju2krona: - - modules/kaiju/kaiju2krona/** - - tests/modules/kaiju/kaiju2krona/** + - modules/nf-core/kaiju/kaiju2krona/** + - tests/modules/nf-core/kaiju/kaiju2krona/** kaiju/kaiju2table: - - modules/kaiju/kaiju2table/** - - tests/modules/kaiju/kaiju2table/** + - modules/nf-core/kaiju/kaiju2table/** + - tests/modules/nf-core/kaiju/kaiju2table/** kallisto/index: - - modules/kallisto/index/** - - tests/modules/kallisto/index/** + - modules/nf-core/kallisto/index/** + - tests/modules/nf-core/kallisto/index/** kallistobustools/count: - - modules/kallistobustools/count/** - - tests/modules/kallistobustools/count/** + - modules/nf-core/kallistobustools/count/** + - tests/modules/nf-core/kallistobustools/count/** kallistobustools/ref: - - modules/kallistobustools/ref/** - - tests/modules/kallistobustools/ref/** + - modules/nf-core/kallistobustools/ref/** + - tests/modules/nf-core/kallistobustools/ref/** kat/hist: - - modules/kat/hist/** - - tests/modules/kat/hist/** + - modules/nf-core/kat/hist/** + - tests/modules/nf-core/kat/hist/** khmer/normalizebymedian: - - modules/khmer/normalizebymedian/** - - tests/modules/khmer/normalizebymedian/** + - modules/nf-core/khmer/normalizebymedian/** + - tests/modules/nf-core/khmer/normalizebymedian/** khmer/uniquekmers: - - modules/khmer/uniquekmers/** - - tests/modules/khmer/uniquekmers/** + - modules/nf-core/khmer/uniquekmers/** + - tests/modules/nf-core/khmer/uniquekmers/** kleborate: - - modules/kleborate/** - - tests/modules/kleborate/** + - modules/nf-core/kleborate/** + - tests/modules/nf-core/kleborate/** kraken2/kraken2: - - modules/kraken2/kraken2/** - - modules/untar/** - - tests/modules/kraken2/kraken2/** + - modules/nf-core/kraken2/kraken2/** + - modules/nf-core/untar/** + - tests/modules/nf-core/kraken2/kraken2/** krakentools/combinekreports: - - modules/krakentools/combinekreports/** - - tests/modules/krakentools/combinekreports/** + - modules/nf-core/krakentools/combinekreports/** + - tests/modules/nf-core/krakentools/combinekreports/** krakentools/kreport2krona: - - modules/krakentools/kreport2krona/** - - tests/modules/krakentools/kreport2krona/** + - modules/nf-core/krakentools/kreport2krona/** + - tests/modules/nf-core/krakentools/kreport2krona/** krona/kronadb: - - modules/krona/kronadb/** - - tests/modules/krona/kronadb/** + - modules/nf-core/krona/kronadb/** + - tests/modules/nf-core/krona/kronadb/** krona/ktimporttaxonomy: - - modules/krona/ktimporttaxonomy/** - - tests/modules/krona/ktimporttaxonomy/** + - modules/nf-core/krona/ktimporttaxonomy/** + - tests/modules/nf-core/krona/ktimporttaxonomy/** krona/ktimporttext: - - modules/krona/ktimporttext/** - - tests/modules/krona/ktimporttext/** + - modules/nf-core/krona/ktimporttext/** + - tests/modules/nf-core/krona/ktimporttext/** krona/ktupdatetaxonomy: - - modules/krona/ktupdatetaxonomy/** - - tests/modules/krona/ktupdatetaxonomy/** + - modules/nf-core/krona/ktupdatetaxonomy/** + - tests/modules/nf-core/krona/ktupdatetaxonomy/** last/dotplot: - - modules/last/dotplot/** - - tests/modules/last/dotplot/** + - modules/nf-core/last/dotplot/** + - tests/modules/nf-core/last/dotplot/** last/lastal: - - modules/last/lastal/** - - tests/modules/last/lastal/** + - modules/nf-core/last/lastal/** + - tests/modules/nf-core/last/lastal/** last/lastdb: - - modules/last/lastdb/** - - tests/modules/last/lastdb/** + - modules/nf-core/last/lastdb/** + - tests/modules/nf-core/last/lastdb/** last/mafconvert: - - modules/last/mafconvert/** - - tests/modules/last/mafconvert/** + - modules/nf-core/last/mafconvert/** + - tests/modules/nf-core/last/mafconvert/** last/mafswap: - - modules/last/mafswap/** - - tests/modules/last/mafswap/** + - modules/nf-core/last/mafswap/** + - tests/modules/nf-core/last/mafswap/** last/postmask: - - modules/last/postmask/** - - tests/modules/last/postmask/** + - modules/nf-core/last/postmask/** + - tests/modules/nf-core/last/postmask/** last/split: - - modules/last/split/** - - tests/modules/last/split/** + - modules/nf-core/last/split/** + - tests/modules/nf-core/last/split/** last/train: - - modules/last/train/** - - tests/modules/last/train/** + - modules/nf-core/last/train/** + - tests/modules/nf-core/last/train/** leehom: - - modules/leehom/** - - tests/modules/leehom/** + - modules/nf-core/leehom/** + - tests/modules/nf-core/leehom/** legsta: - - modules/legsta/** - - tests/modules/legsta/** + - modules/nf-core/legsta/** + - tests/modules/nf-core/legsta/** lima: - - modules/lima/** - - tests/modules/lima/** + - modules/nf-core/lima/** + - tests/modules/nf-core/lima/** lissero: - - modules/lissero/** - - tests/modules/lissero/** + - modules/nf-core/lissero/** + - tests/modules/nf-core/lissero/** lofreq/call: - - modules/lofreq/call/** - - tests/modules/lofreq/call/** + - modules/nf-core/lofreq/call/** + - tests/modules/nf-core/lofreq/call/** lofreq/callparallel: - - modules/lofreq/callparallel/** - - tests/modules/lofreq/callparallel/** + - modules/nf-core/lofreq/callparallel/** + - tests/modules/nf-core/lofreq/callparallel/** lofreq/filter: - - modules/lofreq/filter/** - - tests/modules/lofreq/filter/** + - modules/nf-core/lofreq/filter/** + - tests/modules/nf-core/lofreq/filter/** lofreq/indelqual: - - modules/lofreq/indelqual/** - - tests/modules/lofreq/indelqual/** + - modules/nf-core/lofreq/indelqual/** + - tests/modules/nf-core/lofreq/indelqual/** macrel/contigs: - - modules/macrel/contigs/** - - tests/modules/macrel/contigs/** + - modules/nf-core/macrel/contigs/** + - tests/modules/nf-core/macrel/contigs/** macs2/callpeak: - - modules/macs2/callpeak/** - - tests/modules/macs2/callpeak/** + - modules/nf-core/macs2/callpeak/** + - tests/modules/nf-core/macs2/callpeak/** mafft: - - modules/mafft/** - - tests/modules/mafft/** + - modules/nf-core/mafft/** + - tests/modules/nf-core/mafft/** malt/build: - - modules/malt/build/** - - tests/modules/malt/build_test/** + - modules/nf-core/malt/build/** + - tests/modules/nf-core/malt/build_test/** malt/run: - - modules/malt/run/** - - tests/modules/malt/run/** + - modules/nf-core/malt/run/** + - tests/modules/nf-core/malt/run/** maltextract: - - modules/maltextract/** - - tests/modules/maltextract/** + - modules/nf-core/maltextract/** + - tests/modules/nf-core/maltextract/** manta/convertinversion: - - modules/manta/convertinversion/** - - tests/modules/manta/convertinversion/** + - modules/nf-core/manta/convertinversion/** + - tests/modules/nf-core/manta/convertinversion/** manta/germline: - - modules/manta/germline/** - - tests/modules/manta/germline/** + - modules/nf-core/manta/germline/** + - tests/modules/nf-core/manta/germline/** manta/somatic: - - modules/manta/somatic/** - - tests/modules/manta/somatic/** + - modules/nf-core/manta/somatic/** + - tests/modules/nf-core/manta/somatic/** manta/tumoronly: - - modules/manta/tumoronly/** - - tests/modules/manta/tumoronly/** + - modules/nf-core/manta/tumoronly/** + - tests/modules/nf-core/manta/tumoronly/** mapdamage2: - - modules/mapdamage2/** - - tests/modules/mapdamage2/** + - modules/nf-core/mapdamage2/** + - tests/modules/nf-core/mapdamage2/** mash/dist: - - modules/mash/dist/** - - tests/modules/mash/dist/** + - modules/nf-core/mash/dist/** + - tests/modules/nf-core/mash/dist/** mash/screen: - - modules/mash/screen/** - - tests/modules/mash/screen/** + - modules/nf-core/mash/screen/** + - tests/modules/nf-core/mash/screen/** mash/sketch: - - modules/mash/sketch/** - - tests/modules/mash/sketch/** + - modules/nf-core/mash/sketch/** + - tests/modules/nf-core/mash/sketch/** mashtree: - - modules/mashtree/** - - tests/modules/mashtree/** + - modules/nf-core/mashtree/** + - tests/modules/nf-core/mashtree/** maxbin2: - - modules/maxbin2/** - - tests/modules/maxbin2/** + - modules/nf-core/maxbin2/** + - tests/modules/nf-core/maxbin2/** maxquant/lfq: - - modules/maxquant/lfq/** - - tests/modules/maxquant/lfq/** + - modules/nf-core/maxquant/lfq/** + - tests/modules/nf-core/maxquant/lfq/** mcroni: - - modules/mcroni/** - - tests/modules/mcroni/** + - modules/nf-core/mcroni/** + - tests/modules/nf-core/mcroni/** md5sum: - - modules/md5sum/** - - tests/modules/md5sum/** + - modules/nf-core/md5sum/** + - tests/modules/nf-core/md5sum/** medaka: - - modules/medaka/** - - tests/modules/medaka/** + - modules/nf-core/medaka/** + - tests/modules/nf-core/medaka/** megahit: - - modules/megahit/** - - tests/modules/megahit/** + - modules/nf-core/megahit/** + - tests/modules/nf-core/megahit/** megan/daa2info: - - modules/megan/daa2info/** - - tests/modules/megan/daa2info/** + - modules/nf-core/megan/daa2info/** + - tests/modules/nf-core/megan/daa2info/** megan/rma2info: - - modules/megan/rma2info/** - - tests/modules/megan/rma2info/** + - modules/nf-core/megan/rma2info/** + - tests/modules/nf-core/megan/rma2info/** meningotype: - - modules/meningotype/** - - tests/modules/meningotype/** + - modules/nf-core/meningotype/** + - tests/modules/nf-core/meningotype/** merqury: - - modules/merqury/** - - tests/modules/merqury/** + - modules/nf-core/merqury/** + - tests/modules/nf-core/merqury/** merquryfk/katcomp: - - modules/merquryfk/katcomp/** - - tests/modules/merquryfk/katcomp/** + - modules/nf-core/merquryfk/katcomp/** + - tests/modules/nf-core/merquryfk/katcomp/** merquryfk/katgc: - - modules/merquryfk/katgc/** - - tests/modules/merquryfk/katgc/** + - modules/nf-core/merquryfk/katgc/** + - tests/modules/nf-core/merquryfk/katgc/** merquryfk/merquryfk: - - modules/merquryfk/merquryfk/** - - tests/modules/merquryfk/merquryfk/** + - modules/nf-core/merquryfk/merquryfk/** + - tests/modules/nf-core/merquryfk/merquryfk/** merquryfk/ploidyplot: - - modules/merquryfk/ploidyplot/** - - tests/modules/merquryfk/ploidyplot/** + - modules/nf-core/merquryfk/ploidyplot/** + - tests/modules/nf-core/merquryfk/ploidyplot/** meryl/count: - - modules/meryl/count/** - - tests/modules/meryl/count/** + - modules/nf-core/meryl/count/** + - tests/modules/nf-core/meryl/count/** meryl/histogram: - - modules/meryl/histogram/** - - tests/modules/meryl/histogram/** + - modules/nf-core/meryl/histogram/** + - tests/modules/nf-core/meryl/histogram/** meryl/unionsum: - - modules/meryl/unionsum/** - - tests/modules/meryl/unionsum/** + - modules/nf-core/meryl/unionsum/** + - tests/modules/nf-core/meryl/unionsum/** metabat2/jgisummarizebamcontigdepths: - - modules/metabat2/jgisummarizebamcontigdepths/** - - tests/modules/metabat2/jgisummarizebamcontigdepths/** + - modules/nf-core/metabat2/jgisummarizebamcontigdepths/** + - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/** metabat2/metabat2: - - modules/metabat2/metabat2/** - - tests/modules/metabat2/metabat2/** + - modules/nf-core/metabat2/metabat2/** + - tests/modules/nf-core/metabat2/metabat2/** metaphlan3/mergemetaphlantables: - - modules/metaphlan3/mergemetaphlantables/** - - tests/modules/metaphlan3/mergemetaphlantables/** + - modules/nf-core/metaphlan3/mergemetaphlantables/** + - tests/modules/nf-core/metaphlan3/mergemetaphlantables/** metaphlan3/metaphlan3: - - modules/metaphlan3/metaphlan3/** - - tests/modules/metaphlan3/metaphlan3/** + - modules/nf-core/metaphlan3/metaphlan3/** + - tests/modules/nf-core/metaphlan3/metaphlan3/** methyldackel/extract: - - modules/methyldackel/extract/** - - tests/modules/methyldackel/extract/** + - modules/nf-core/methyldackel/extract/** + - tests/modules/nf-core/methyldackel/extract/** methyldackel/mbias: - - modules/methyldackel/mbias/** - - tests/modules/methyldackel/mbias/** + - modules/nf-core/methyldackel/mbias/** + - tests/modules/nf-core/methyldackel/mbias/** minia: - - modules/minia/** - - tests/modules/minia/** + - modules/nf-core/minia/** + - tests/modules/nf-core/minia/** miniasm: - - modules/miniasm/** - - tests/modules/miniasm/** + - modules/nf-core/miniasm/** + - tests/modules/nf-core/miniasm/** minimap2/align: - - modules/minimap2/align/** - - tests/modules/minimap2/align/** + - modules/nf-core/minimap2/align/** + - tests/modules/nf-core/minimap2/align/** minimap2/index: - - modules/minimap2/index/** - - tests/modules/minimap2/index/** + - modules/nf-core/minimap2/index/** + - tests/modules/nf-core/minimap2/index/** mlst: - - modules/mlst/** - - tests/modules/mlst/** + - modules/nf-core/mlst/** + - tests/modules/nf-core/mlst/** mobsuite/recon: - - modules/mobsuite/recon/** - - tests/modules/mobsuite/recon/** + - modules/nf-core/mobsuite/recon/** + - tests/modules/nf-core/mobsuite/recon/** mosdepth: - - modules/mosdepth/** - - tests/modules/mosdepth/** + - modules/nf-core/mosdepth/** + - tests/modules/nf-core/mosdepth/** motus/downloaddb: - - modules/motus/downloaddb/** - - tests/modules/motus/downloaddb/** + - modules/nf-core/motus/downloaddb/** + - tests/modules/nf-core/motus/downloaddb/** motus/merge: - - modules/motus/merge/** - - tests/modules/motus/merge/** + - modules/nf-core/motus/merge/** + - tests/modules/nf-core/motus/merge/** motus/profile: - - modules/motus/profile/** - - tests/modules/motus/profile/** + - modules/nf-core/motus/profile/** + - tests/modules/nf-core/motus/profile/** msisensor/msi: - - modules/msisensor/msi/** - - tests/modules/msisensor/msi/** + - modules/nf-core/msisensor/msi/** + - tests/modules/nf-core/msisensor/msi/** msisensor/scan: - - modules/msisensor/scan/** - - tests/modules/msisensor/scan/** + - modules/nf-core/msisensor/scan/** + - tests/modules/nf-core/msisensor/scan/** msisensor2/msi: - - modules/msisensor2/msi/** - - tests/modules/msisensor2/msi/** + - modules/nf-core/msisensor2/msi/** + - tests/modules/nf-core/msisensor2/msi/** msisensor2/scan: - - modules/msisensor2/scan/** - - tests/modules/msisensor2/scan/** + - modules/nf-core/msisensor2/scan/** + - tests/modules/nf-core/msisensor2/scan/** msisensorpro/msi_somatic: - - modules/msisensorpro/msi_somatic/** - - tests/modules/msisensorpro/msi_somatic/** + - modules/nf-core/msisensorpro/msi_somatic/** + - tests/modules/nf-core/msisensorpro/msi_somatic/** msisensorpro/scan: - - modules/msisensorpro/scan/** - - tests/modules/msisensorpro/scan/** + - modules/nf-core/msisensorpro/scan/** + - tests/modules/nf-core/msisensorpro/scan/** mtnucratio: - - modules/mtnucratio/** - - tests/modules/mtnucratio/** + - modules/nf-core/mtnucratio/** + - tests/modules/nf-core/mtnucratio/** multiqc: - - modules/fastqc/** - - modules/multiqc/** - - tests/modules/multiqc/** + - modules/nf-core/fastqc/** + - modules/nf-core/multiqc/** + - tests/modules/nf-core/multiqc/** multivcfanalyzer: - - modules/multivcfanalyzer/** - - tests/modules/multivcfanalyzer/** + - modules/nf-core/multivcfanalyzer/** + - tests/modules/nf-core/multivcfanalyzer/** mummer: - - modules/mummer/** - - tests/modules/mummer/** + - modules/nf-core/mummer/** + - tests/modules/nf-core/mummer/** muscle: - - modules/muscle/** - - tests/modules/muscle/** + - modules/nf-core/muscle/** + - tests/modules/nf-core/muscle/** mykrobe/predict: - - modules/mykrobe/predict/** - - tests/modules/mykrobe/predict/** + - modules/nf-core/mykrobe/predict/** + - tests/modules/nf-core/mykrobe/predict/** nanolyse: - - modules/nanolyse/** - - tests/modules/nanolyse/** + - modules/nf-core/nanolyse/** + - tests/modules/nf-core/nanolyse/** nanoplot: - - modules/nanoplot/** - - tests/modules/nanoplot/** + - modules/nf-core/nanoplot/** + - tests/modules/nf-core/nanoplot/** ncbigenomedownload: - - modules/ncbigenomedownload/** - - tests/modules/ncbigenomedownload/** + - modules/nf-core/ncbigenomedownload/** + - tests/modules/nf-core/ncbigenomedownload/** nextclade/datasetget: - - modules/nextclade/datasetget/** - - tests/modules/nextclade/datasetget/** + - modules/nf-core/nextclade/datasetget/** + - tests/modules/nf-core/nextclade/datasetget/** nextclade/run: - - modules/nextclade/run/** - - tests/modules/nextclade/run/** + - modules/nf-core/nextclade/run/** + - tests/modules/nf-core/nextclade/run/** nextgenmap: - - modules/nextgenmap/** - - tests/modules/nextgenmap/** + - modules/nf-core/nextgenmap/** + - tests/modules/nf-core/nextgenmap/** ngmaster: - - modules/ngmaster/** - - tests/modules/ngmaster/** + - modules/nf-core/ngmaster/** + - tests/modules/nf-core/ngmaster/** ngscheckmate/ncm: - - modules/ngscheckmate/ncm/** - - tests/modules/ngscheckmate/ncm/** + - modules/nf-core/ngscheckmate/ncm/** + - tests/modules/nf-core/ngscheckmate/ncm/** nucmer: - - modules/nucmer/** - - tests/modules/nucmer/** + - modules/nf-core/nucmer/** + - tests/modules/nf-core/nucmer/** optitype: - - modules/optitype/** - - tests/modules/optitype/** + - modules/nf-core/optitype/** + - tests/modules/nf-core/optitype/** pairix: - - modules/pairix/** - - tests/modules/pairix/** + - modules/nf-core/pairix/** + - tests/modules/nf-core/pairix/** pairtools/dedup: - - modules/pairtools/dedup/** - - tests/modules/pairtools/dedup/** + - modules/nf-core/pairtools/dedup/** + - tests/modules/nf-core/pairtools/dedup/** pairtools/flip: - - modules/pairtools/flip/** - - tests/modules/pairtools/flip/** + - modules/nf-core/pairtools/flip/** + - tests/modules/nf-core/pairtools/flip/** pairtools/parse: - - modules/pairtools/parse/** - - tests/modules/pairtools/parse/** + - modules/nf-core/pairtools/parse/** + - tests/modules/nf-core/pairtools/parse/** pairtools/restrict: - - modules/pairtools/restrict/** - - tests/modules/pairtools/restrict/** + - modules/nf-core/pairtools/restrict/** + - tests/modules/nf-core/pairtools/restrict/** pairtools/select: - - modules/pairtools/select/** - - tests/modules/pairtools/select/** + - modules/nf-core/pairtools/select/** + - tests/modules/nf-core/pairtools/select/** pairtools/sort: - - modules/pairtools/sort/** - - tests/modules/pairtools/sort/** + - modules/nf-core/pairtools/sort/** + - tests/modules/nf-core/pairtools/sort/** panaroo/run: - - modules/panaroo/run/** - - tests/modules/panaroo/run/** + - modules/nf-core/panaroo/run/** + - tests/modules/nf-core/panaroo/run/** pangolin: - - modules/pangolin/** - - tests/modules/pangolin/** + - modules/nf-core/pangolin/** + - tests/modules/nf-core/pangolin/** paraclu: - - modules/paraclu/** - - tests/modules/paraclu/** + - modules/nf-core/paraclu/** + - tests/modules/nf-core/paraclu/** pasty: - - modules/pasty/** - - tests/modules/pasty/** + - modules/nf-core/pasty/** + - tests/modules/nf-core/pasty/** pbbam/pbmerge: - - modules/pbbam/pbmerge/** - - tests/modules/pbbam/pbmerge/** + - modules/nf-core/pbbam/pbmerge/** + - tests/modules/nf-core/pbbam/pbmerge/** pbccs: - - modules/pbccs/** - - tests/modules/pbccs/** + - modules/nf-core/pbccs/** + - tests/modules/nf-core/pbccs/** pbptyper: - - modules/pbptyper/** - - tests/modules/pbptyper/** + - modules/nf-core/pbptyper/** + - tests/modules/nf-core/pbptyper/** pear: - - modules/pear/** - - tests/modules/pear/** + - modules/nf-core/pear/** + - tests/modules/nf-core/pear/** peddy: - - modules/peddy/** - - tests/modules/peddy/** + - modules/nf-core/peddy/** + - tests/modules/nf-core/peddy/** phantompeakqualtools: - - modules/phantompeakqualtools/** - - tests/modules/phantompeakqualtools/** + - modules/nf-core/phantompeakqualtools/** + - tests/modules/nf-core/phantompeakqualtools/** phyloflash: - - modules/phyloflash/** - - tests/modules/phyloflash/** + - modules/nf-core/phyloflash/** + - tests/modules/nf-core/phyloflash/** picard/addorreplacereadgroups: - - modules/picard/addorreplacereadgroups/** - - tests/modules/picard/addorreplacereadgroups/** + - modules/nf-core/picard/addorreplacereadgroups/** + - tests/modules/nf-core/picard/addorreplacereadgroups/** picard/cleansam: - - modules/picard/cleansam/** - - tests/modules/picard/cleansam/** + - modules/nf-core/picard/cleansam/** + - tests/modules/nf-core/picard/cleansam/** picard/collecthsmetrics: - - modules/picard/collecthsmetrics/** - - tests/modules/picard/collecthsmetrics/** + - modules/nf-core/picard/collecthsmetrics/** + - tests/modules/nf-core/picard/collecthsmetrics/** picard/collectmultiplemetrics: - - modules/picard/collectmultiplemetrics/** - - tests/modules/picard/collectmultiplemetrics/** + - modules/nf-core/picard/collectmultiplemetrics/** + - tests/modules/nf-core/picard/collectmultiplemetrics/** picard/collectwgsmetrics: - - modules/picard/collectwgsmetrics/** - - tests/modules/picard/collectwgsmetrics/** + - modules/nf-core/picard/collectwgsmetrics/** + - tests/modules/nf-core/picard/collectwgsmetrics/** picard/createsequencedictionary: - - modules/picard/createsequencedictionary/** - - tests/modules/picard/createsequencedictionary/** + - modules/nf-core/picard/createsequencedictionary/** + - tests/modules/nf-core/picard/createsequencedictionary/** picard/crosscheckfingerprints: - - modules/picard/crosscheckfingerprints/** - - tests/modules/picard/crosscheckfingerprints/** + - modules/nf-core/picard/crosscheckfingerprints/** + - tests/modules/nf-core/picard/crosscheckfingerprints/** picard/fastqtosam: - - modules/picard/fastqtosam/** - - tests/modules/picard/fastqtosam/** + - modules/nf-core/picard/fastqtosam/** + - tests/modules/nf-core/picard/fastqtosam/** picard/filtersamreads: - - modules/picard/filtersamreads/** - - tests/modules/picard/filtersamreads/** + - modules/nf-core/picard/filtersamreads/** + - tests/modules/nf-core/picard/filtersamreads/** picard/fixmateinformation: - - modules/picard/fixmateinformation/** - - tests/modules/picard/fixmateinformation/** + - modules/nf-core/picard/fixmateinformation/** + - tests/modules/nf-core/picard/fixmateinformation/** picard/liftovervcf: - - modules/picard/liftovervcf/** - - tests/modules/picard/liftovervcf/** + - modules/nf-core/picard/liftovervcf/** + - tests/modules/nf-core/picard/liftovervcf/** picard/markduplicates: - - modules/picard/markduplicates/** - - tests/modules/picard/markduplicates/** + - modules/nf-core/picard/markduplicates/** + - tests/modules/nf-core/picard/markduplicates/** picard/mergesamfiles: - - modules/picard/mergesamfiles/** - - tests/modules/picard/mergesamfiles/** + - modules/nf-core/picard/mergesamfiles/** + - tests/modules/nf-core/picard/mergesamfiles/** picard/sortsam: - - modules/picard/sortsam/** - - tests/modules/picard/sortsam/** + - modules/nf-core/picard/sortsam/** + - tests/modules/nf-core/picard/sortsam/** picard/sortvcf: - - modules/picard/sortvcf/** - - tests/modules/picard/sortvcf/** + - modules/nf-core/picard/sortvcf/** + - tests/modules/nf-core/picard/sortvcf/** pints/caller: - - modules/pints/caller/** - - tests/modules/pints/caller/** + - modules/nf-core/pints/caller/** + - tests/modules/nf-core/pints/caller/** pirate: - - modules/pirate/** - - tests/modules/pirate/** + - modules/nf-core/pirate/** + - tests/modules/nf-core/pirate/** plasmidfinder: - - modules/plasmidfinder/** - - tests/modules/plasmidfinder/** + - modules/nf-core/plasmidfinder/** + - tests/modules/nf-core/plasmidfinder/** plasmidid: - - modules/plasmidid/** - - tests/modules/plasmidid/** + - modules/nf-core/plasmidid/** + - tests/modules/nf-core/plasmidid/** plink/extract: - - modules/plink/extract/** - - tests/modules/plink/extract/** + - modules/nf-core/plink/extract/** + - tests/modules/nf-core/plink/extract/** plink/vcf: - - modules/plink/vcf/** - - tests/modules/plink/vcf/** + - modules/nf-core/plink/vcf/** + - tests/modules/nf-core/plink/vcf/** plink2/extract: - - modules/plink2/extract/** - - tests/modules/plink2/extract/** + - modules/nf-core/plink2/extract/** + - tests/modules/nf-core/plink2/extract/** plink2/score: - - modules/plink2/score/** - - tests/modules/plink2/score/** + - modules/nf-core/plink2/score/** + - tests/modules/nf-core/plink2/score/** plink2/vcf: - - modules/plink2/vcf/** - - tests/modules/plink2/vcf/** + - modules/nf-core/plink2/vcf/** + - tests/modules/nf-core/plink2/vcf/** pmdtools/filter: - - modules/pmdtools/filter/** - - tests/modules/pmdtools/filter/** + - modules/nf-core/pmdtools/filter/** + - tests/modules/nf-core/pmdtools/filter/** porechop: - - modules/porechop/** - - tests/modules/porechop/** + - modules/nf-core/porechop/** + - tests/modules/nf-core/porechop/** preseq/ccurve: - - modules/preseq/ccurve/** - - tests/modules/preseq/ccurve/** + - modules/nf-core/preseq/ccurve/** + - tests/modules/nf-core/preseq/ccurve/** preseq/lcextrap: - - modules/preseq/lcextrap/** - - tests/modules/preseq/lcextrap/** + - modules/nf-core/preseq/lcextrap/** + - tests/modules/nf-core/preseq/lcextrap/** prinseqplusplus: - - modules/prinseqplusplus/** - - tests/modules/prinseqplusplus/** + - modules/nf-core/prinseqplusplus/** + - tests/modules/nf-core/prinseqplusplus/** prodigal: - - modules/prodigal/** - - tests/modules/prodigal/** + - modules/nf-core/prodigal/** + - tests/modules/nf-core/prodigal/** prokka: - - modules/prokka/** - - tests/modules/prokka/** + - modules/nf-core/prokka/** + - tests/modules/nf-core/prokka/** pycoqc: - - modules/pycoqc/** - - tests/modules/pycoqc/** + - modules/nf-core/pycoqc/** + - tests/modules/nf-core/pycoqc/** pydamage/analyze: - - modules/pydamage/analyze/** - - tests/modules/pydamage/analyze/** + - modules/nf-core/pydamage/analyze/** + - tests/modules/nf-core/pydamage/analyze/** pydamage/filter: - - modules/pydamage/filter/** - - tests/modules/pydamage/filter/** + - modules/nf-core/pydamage/filter/** + - tests/modules/nf-core/pydamage/filter/** qcat: - - modules/qcat/** - - tests/modules/qcat/** + - modules/nf-core/qcat/** + - tests/modules/nf-core/qcat/** qualimap/bamqc: - - modules/qualimap/bamqc/** - - tests/modules/qualimap/bamqc/** + - modules/nf-core/qualimap/bamqc/** + - tests/modules/nf-core/qualimap/bamqc/** qualimap/bamqccram: - - modules/qualimap/bamqccram/** - - tests/modules/qualimap/bamqccram/** + - modules/nf-core/qualimap/bamqccram/** + - tests/modules/nf-core/qualimap/bamqccram/** quast: - - modules/quast/** - - tests/modules/quast/** + - modules/nf-core/quast/** + - tests/modules/nf-core/quast/** racon: - - modules/racon/** - - tests/modules/racon/** + - modules/nf-core/racon/** + - tests/modules/nf-core/racon/** rapidnj: - - modules/rapidnj/** - - tests/modules/rapidnj/** + - modules/nf-core/rapidnj/** + - tests/modules/nf-core/rapidnj/** rasusa: - - modules/rasusa/** - - tests/modules/rasusa/** + - modules/nf-core/rasusa/** + - tests/modules/nf-core/rasusa/** raven: - - modules/raven/** - - tests/modules/raven/** + - modules/nf-core/raven/** + - tests/modules/nf-core/raven/** raxmlng: - - modules/raxmlng/** - - tests/modules/raxmlng/** + - modules/nf-core/raxmlng/** + - tests/modules/nf-core/raxmlng/** rgi/main: - - modules/rgi/main/** - - tests/modules/rgi/main/** + - modules/nf-core/rgi/main/** + - tests/modules/nf-core/rgi/main/** rhocall/annotate: - - modules/rhocall/annotate/** - - tests/modules/rhocall/annotate/** + - modules/nf-core/rhocall/annotate/** + - tests/modules/nf-core/rhocall/annotate/** rmarkdownnotebook: - - modules/rmarkdownnotebook/** - - tests/modules/rmarkdownnotebook/** + - modules/nf-core/rmarkdownnotebook/** + - tests/modules/nf-core/rmarkdownnotebook/** roary: - - modules/roary/** - - tests/modules/roary/** + - modules/nf-core/roary/** + - tests/modules/nf-core/roary/** rsem/calculateexpression: - - modules/rsem/calculateexpression/** - - tests/modules/rsem/calculateexpression/** + - modules/nf-core/rsem/calculateexpression/** + - tests/modules/nf-core/rsem/calculateexpression/** rsem/preparereference: - - modules/rsem/preparereference/** - - tests/modules/rsem/preparereference/** + - modules/nf-core/rsem/preparereference/** + - tests/modules/nf-core/rsem/preparereference/** rseqc/bamstat: - - modules/rseqc/bamstat/** - - tests/modules/rseqc/bamstat/** + - modules/nf-core/rseqc/bamstat/** + - tests/modules/nf-core/rseqc/bamstat/** rseqc/inferexperiment: - - modules/rseqc/inferexperiment/** - - tests/modules/rseqc/inferexperiment/** + - modules/nf-core/rseqc/inferexperiment/** + - tests/modules/nf-core/rseqc/inferexperiment/** rseqc/innerdistance: - - modules/rseqc/innerdistance/** - - tests/modules/rseqc/innerdistance/** + - modules/nf-core/rseqc/innerdistance/** + - tests/modules/nf-core/rseqc/innerdistance/** rseqc/junctionannotation: - - modules/rseqc/junctionannotation/** - - tests/modules/rseqc/junctionannotation/** + - modules/nf-core/rseqc/junctionannotation/** + - tests/modules/nf-core/rseqc/junctionannotation/** rseqc/junctionsaturation: - - modules/rseqc/junctionsaturation/** - - tests/modules/rseqc/junctionsaturation/** + - modules/nf-core/rseqc/junctionsaturation/** + - tests/modules/nf-core/rseqc/junctionsaturation/** rseqc/readdistribution: - - modules/rseqc/readdistribution/** - - tests/modules/rseqc/readdistribution/** + - modules/nf-core/rseqc/readdistribution/** + - tests/modules/nf-core/rseqc/readdistribution/** rseqc/readduplication: - - modules/rseqc/readduplication/** - - tests/modules/rseqc/readduplication/** + - modules/nf-core/rseqc/readduplication/** + - tests/modules/nf-core/rseqc/readduplication/** rseqc/tin: - - modules/rseqc/tin/** - - tests/modules/rseqc/tin/** + - modules/nf-core/rseqc/tin/** + - tests/modules/nf-core/rseqc/tin/** rtgtools/pedfilter: - - modules/rtgtools/pedfilter/** - - tests/modules/rtgtools/pedfilter/** + - modules/nf-core/rtgtools/pedfilter/** + - tests/modules/nf-core/rtgtools/pedfilter/** rtgtools/vcfeval: - - modules/rtgtools/vcfeval/** - - tests/modules/rtgtools/vcfeval/** + - modules/nf-core/rtgtools/vcfeval/** + - tests/modules/nf-core/rtgtools/vcfeval/** salmon/index: - - modules/salmon/index/** - - tests/modules/salmon/index/** + - modules/nf-core/salmon/index/** + - tests/modules/nf-core/salmon/index/** salmon/quant: - - modules/salmon/quant/** - - tests/modules/salmon/quant/** + - modules/nf-core/salmon/quant/** + - tests/modules/nf-core/salmon/quant/** samblaster: - - modules/samblaster/** - - tests/modules/samblaster/** + - modules/nf-core/samblaster/** + - tests/modules/nf-core/samblaster/** samtools/ampliconclip: - - modules/samtools/ampliconclip/** - - tests/modules/samtools/ampliconclip/** + - modules/nf-core/samtools/ampliconclip/** + - tests/modules/nf-core/samtools/ampliconclip/** samtools/bam2fq: - - modules/samtools/bam2fq/** - - tests/modules/samtools/bam2fq/** + - modules/nf-core/samtools/bam2fq/** + - tests/modules/nf-core/samtools/bam2fq/** samtools/collate: - - modules/samtools/collate/** - - tests/modules/samtools/collate/** + - modules/nf-core/samtools/collate/** + - tests/modules/nf-core/samtools/collate/** samtools/collatefastq: - - modules/samtools/collatefastq/** - - tests/modules/samtools/collatefastq/** + - modules/nf-core/samtools/collatefastq/** + - tests/modules/nf-core/samtools/collatefastq/** samtools/convert: - - modules/samtools/convert/** - - tests/modules/samtools/convert/** + - modules/nf-core/samtools/convert/** + - tests/modules/nf-core/samtools/convert/** samtools/depth: - - modules/samtools/depth/** - - tests/modules/samtools/depth/** + - modules/nf-core/samtools/depth/** + - tests/modules/nf-core/samtools/depth/** samtools/dict: - - modules/samtools/dict/** - - tests/modules/samtools/dict/** + - modules/nf-core/samtools/dict/** + - tests/modules/nf-core/samtools/dict/** samtools/faidx: - - modules/samtools/faidx/** - - tests/modules/samtools/faidx/** + - modules/nf-core/samtools/faidx/** + - tests/modules/nf-core/samtools/faidx/** samtools/fasta: - - modules/samtools/fasta/** - - tests/modules/samtools/fasta/** + - modules/nf-core/samtools/fasta/** + - tests/modules/nf-core/samtools/fasta/** samtools/fastq: - - modules/samtools/fastq/** - - tests/modules/samtools/fastq/** + - modules/nf-core/samtools/fastq/** + - tests/modules/nf-core/samtools/fastq/** samtools/fixmate: - - modules/samtools/fixmate/** - - tests/modules/samtools/fixmate/** + - modules/nf-core/samtools/fixmate/** + - tests/modules/nf-core/samtools/fixmate/** samtools/flagstat: - - modules/samtools/flagstat/** - - tests/modules/samtools/flagstat/** + - modules/nf-core/samtools/flagstat/** + - tests/modules/nf-core/samtools/flagstat/** samtools/getrg: - - modules/samtools/getrg/** - - tests/modules/samtools/getrg/** + - modules/nf-core/samtools/getrg/** + - tests/modules/nf-core/samtools/getrg/** samtools/idxstats: - - modules/samtools/idxstats/** - - tests/modules/samtools/idxstats/** + - modules/nf-core/samtools/idxstats/** + - tests/modules/nf-core/samtools/idxstats/** samtools/index: - - modules/samtools/index/** - - tests/modules/samtools/index/** + - modules/nf-core/samtools/index/** + - tests/modules/nf-core/samtools/index/** samtools/markdup: - - modules/samtools/markdup/** - - tests/modules/samtools/markdup/** + - modules/nf-core/samtools/markdup/** + - tests/modules/nf-core/samtools/markdup/** samtools/merge: - - modules/samtools/merge/** - - tests/modules/samtools/merge/** + - modules/nf-core/samtools/merge/** + - tests/modules/nf-core/samtools/merge/** samtools/mpileup: - - modules/samtools/mpileup/** - - tests/modules/samtools/mpileup/** + - modules/nf-core/samtools/mpileup/** + - tests/modules/nf-core/samtools/mpileup/** samtools/sort: - - modules/samtools/sort/** - - tests/modules/samtools/sort/** + - modules/nf-core/samtools/sort/** + - tests/modules/nf-core/samtools/sort/** samtools/stats: - - modules/samtools/stats/** - - tests/modules/samtools/stats/** + - modules/nf-core/samtools/stats/** + - tests/modules/nf-core/samtools/stats/** samtools/view: - - modules/samtools/view/** - - tests/modules/samtools/view/** + - modules/nf-core/samtools/view/** + - tests/modules/nf-core/samtools/view/** scoary: - - modules/scoary/** - - tests/modules/scoary/** + - modules/nf-core/scoary/** + - tests/modules/nf-core/scoary/** scramble/clusteranalysis: - - modules/scramble/clusteranalysis/** - - tests/modules/scramble/clusteranalysis/** + - modules/nf-core/scramble/clusteranalysis/** + - tests/modules/nf-core/scramble/clusteranalysis/** scramble/clusteridentifier: - - modules/scramble/clusteridentifier/** - - tests/modules/scramble/clusteridentifier/** + - modules/nf-core/scramble/clusteridentifier/** + - tests/modules/nf-core/scramble/clusteridentifier/** seacr/callpeak: - - modules/seacr/callpeak/** - - tests/modules/seacr/callpeak/** + - modules/nf-core/seacr/callpeak/** + - tests/modules/nf-core/seacr/callpeak/** seqkit/pair: - - modules/seqkit/pair/** - - tests/modules/seqkit/pair/** + - modules/nf-core/seqkit/pair/** + - tests/modules/nf-core/seqkit/pair/** seqkit/replace: - - modules/seqkit/replace/** - - tests/modules/seqkit/replace/** + - modules/nf-core/seqkit/replace/** + - tests/modules/nf-core/seqkit/replace/** seqkit/split2: - - modules/seqkit/split2/** - - tests/modules/seqkit/split2/** + - modules/nf-core/seqkit/split2/** + - tests/modules/nf-core/seqkit/split2/** seqkit/stats: - - modules/seqkit/stats/** - - tests/modules/seqkit/stats/** + - modules/nf-core/seqkit/stats/** + - tests/modules/nf-core/seqkit/stats/** seqsero2: - - modules/seqsero2/** - - tests/modules/seqsero2/** + - modules/nf-core/seqsero2/** + - tests/modules/nf-core/seqsero2/** seqtk/mergepe: - - modules/seqtk/mergepe/** - - tests/modules/seqtk/mergepe/** + - modules/nf-core/seqtk/mergepe/** + - tests/modules/nf-core/seqtk/mergepe/** seqtk/rename: - - modules/seqtk/rename/** - - tests/modules/seqtk/rename/** + - modules/nf-core/seqtk/rename/** + - tests/modules/nf-core/seqtk/rename/** seqtk/sample: - - modules/seqtk/sample/** - - tests/modules/seqtk/sample/** + - modules/nf-core/seqtk/sample/** + - tests/modules/nf-core/seqtk/sample/** seqtk/seq: - - modules/seqtk/seq/** - - tests/modules/seqtk/seq/** + - modules/nf-core/seqtk/seq/** + - tests/modules/nf-core/seqtk/seq/** seqtk/subseq: - - modules/seqtk/subseq/** - - tests/modules/seqtk/subseq/** + - modules/nf-core/seqtk/subseq/** + - tests/modules/nf-core/seqtk/subseq/** sequenzautils/bam2seqz: - - modules/sequenzautils/bam2seqz/** - - tests/modules/sequenzautils/bam2seqz/** + - modules/nf-core/sequenzautils/bam2seqz/** + - tests/modules/nf-core/sequenzautils/bam2seqz/** sequenzautils/gcwiggle: - - modules/sequenzautils/gcwiggle/** - - tests/modules/sequenzautils/gcwiggle/** + - modules/nf-core/sequenzautils/gcwiggle/** + - tests/modules/nf-core/sequenzautils/gcwiggle/** seqwish/induce: - - modules/seqwish/induce/** - - tests/modules/seqwish/induce/** + - modules/nf-core/seqwish/induce/** + - tests/modules/nf-core/seqwish/induce/** seroba/run: - - modules/seroba/run/** - - tests/modules/seroba/run/** + - modules/nf-core/seroba/run/** + - tests/modules/nf-core/seroba/run/** sexdeterrmine: - - modules/sexdeterrmine/** - - tests/modules/sexdeterrmine/** + - modules/nf-core/sexdeterrmine/** + - tests/modules/nf-core/sexdeterrmine/** shasta: - - modules/shasta/** - - tests/modules/shasta/** + - modules/nf-core/shasta/** + - tests/modules/nf-core/shasta/** shasum: - - modules/shasum/** - - tests/modules/shasum/** + - modules/nf-core/shasum/** + - tests/modules/nf-core/shasum/** shigatyper: - - modules/shigatyper/** - - tests/modules/shigatyper/** + - modules/nf-core/shigatyper/** + - tests/modules/nf-core/shigatyper/** shovill: - - modules/shovill/** - - tests/modules/shovill/** + - modules/nf-core/shovill/** + - tests/modules/nf-core/shovill/** sistr: - - modules/sistr/** - - tests/modules/sistr/** + - modules/nf-core/sistr/** + - tests/modules/nf-core/sistr/** slimfastq: - - modules/slimfastq/** - - tests/modules/slimfastq/** + - modules/nf-core/slimfastq/** + - tests/modules/nf-core/slimfastq/** snapaligner/align: - - modules/snapaligner/align/** - - tests/modules/snapaligner/align/** + - modules/nf-core/snapaligner/align/** + - tests/modules/nf-core/snapaligner/align/** snapaligner/index: - - modules/snapaligner/index/** - - tests/modules/snapaligner/index/** + - modules/nf-core/snapaligner/index/** + - tests/modules/nf-core/snapaligner/index/** snippy/core: - - modules/snippy/core/** - - tests/modules/snippy/core/** + - modules/nf-core/snippy/core/** + - tests/modules/nf-core/snippy/core/** snippy/run: - - modules/snippy/run/** - - tests/modules/snippy/run/** + - modules/nf-core/snippy/run/** + - tests/modules/nf-core/snippy/run/** snpdists: - - modules/snpdists/** - - tests/modules/snpdists/** + - modules/nf-core/snpdists/** + - tests/modules/nf-core/snpdists/** snpeff: - - modules/snpeff/** - - tests/modules/snpeff/** + - modules/nf-core/snpeff/** + - tests/modules/nf-core/snpeff/** snpsift/split: - - modules/snpsift/split/** - - tests/modules/snpsift/split/** + - modules/nf-core/snpsift/split/** + - tests/modules/nf-core/snpsift/split/** snpsites: - - modules/snpsites/** - - tests/modules/snpsites/** + - modules/nf-core/snpsites/** + - tests/modules/nf-core/snpsites/** somalier/extract: - - modules/somalier/extract/** - - tests/modules/somalier/extract/** + - modules/nf-core/somalier/extract/** + - tests/modules/nf-core/somalier/extract/** somalier/relate: - - modules/somalier/relate/** - - tests/modules/somalier/relate/** + - modules/nf-core/somalier/relate/** + - tests/modules/nf-core/somalier/relate/** sourmash/sketch: - - modules/sourmash/sketch/** - - tests/modules/sourmash/sketch/** + - modules/nf-core/sourmash/sketch/** + - tests/modules/nf-core/sourmash/sketch/** spades: - - modules/spades/** - - tests/modules/spades/** + - modules/nf-core/spades/** + - tests/modules/nf-core/spades/** spatyper: - - modules/spatyper/** - - tests/modules/spatyper/** + - modules/nf-core/spatyper/** + - tests/modules/nf-core/spatyper/** sratools/fasterqdump: - - modules/sratools/fasterqdump/** - - tests/modules/sratools/fasterqdump/** + - modules/nf-core/sratools/fasterqdump/** + - tests/modules/nf-core/sratools/fasterqdump/** sratools/prefetch: - - modules/sratools/prefetch/** - - tests/modules/sratools/prefetch/** + - modules/nf-core/sratools/prefetch/** + - tests/modules/nf-core/sratools/prefetch/** srst2/srst2: - - modules/srst2/srst2/** - - tests/modules/srst2/srst2/** + - modules/nf-core/srst2/srst2/** + - tests/modules/nf-core/srst2/srst2/** ssuissero: - - modules/ssuissero/** - - tests/modules/ssuissero/** + - modules/nf-core/ssuissero/** + - tests/modules/nf-core/ssuissero/** stadeniolib/scramble: - - modules/stadeniolib/scramble/** - - tests/modules/stadeniolib/scramble/** + - modules/nf-core/stadeniolib/scramble/** + - tests/modules/nf-core/stadeniolib/scramble/** staphopiasccmec: - - modules/staphopiasccmec/** - - tests/modules/staphopiasccmec/** + - modules/nf-core/staphopiasccmec/** + - tests/modules/nf-core/staphopiasccmec/** star/align: - - modules/star/align/** - - tests/modules/star/align/** + - modules/nf-core/star/align/** + - tests/modules/nf-core/star/align/** star/genomegenerate: - - modules/star/genomegenerate/** - - tests/modules/star/genomegenerate/** + - modules/nf-core/star/genomegenerate/** + - tests/modules/nf-core/star/genomegenerate/** stranger: - - modules/stranger/** - - tests/modules/stranger/** + - modules/nf-core/stranger/** + - tests/modules/nf-core/stranger/** strelka/germline: - - modules/strelka/germline/** - - tests/modules/strelka/germline/** + - modules/nf-core/strelka/germline/** + - tests/modules/nf-core/strelka/germline/** strelka/somatic: - - modules/strelka/somatic/** - - tests/modules/strelka/somatic/** + - modules/nf-core/strelka/somatic/** + - tests/modules/nf-core/strelka/somatic/** stringtie/merge: - - modules/stringtie/merge/** - - tests/modules/stringtie/merge/** + - modules/nf-core/stringtie/merge/** + - tests/modules/nf-core/stringtie/merge/** stringtie/stringtie: - - modules/stringtie/stringtie/** - - tests/modules/stringtie/stringtie/** + - modules/nf-core/stringtie/stringtie/** + - tests/modules/nf-core/stringtie/stringtie/** subread/featurecounts: - - modules/subread/featurecounts/** - - tests/modules/subread/featurecounts/** + - modules/nf-core/subread/featurecounts/** + - tests/modules/nf-core/subread/featurecounts/** subworkflows/bam_stats_samtools: - subworkflows/nf-core/bam_stats_samtools/** - tests/subworkflows/nf-core/bam_stats_samtools/** svdb/merge: - - modules/svdb/merge/** - - tests/modules/svdb/merge/** + - modules/nf-core/svdb/merge/** + - tests/modules/nf-core/svdb/merge/** svdb/query: - - modules/svdb/query/** - - tests/modules/svdb/query/** + - modules/nf-core/svdb/query/** + - tests/modules/nf-core/svdb/query/** svtk/standardize: - - modules/svtk/standardize/** - - tests/modules/svtk/standardize/** + - modules/nf-core/svtk/standardize/** + - tests/modules/nf-core/svtk/standardize/** tabix/bgzip: - - modules/tabix/bgzip/** - - tests/modules/tabix/bgzip/** + - modules/nf-core/tabix/bgzip/** + - tests/modules/nf-core/tabix/bgzip/** tabix/bgziptabix: - - modules/tabix/bgziptabix/** - - tests/modules/tabix/bgziptabix/** + - modules/nf-core/tabix/bgziptabix/** + - tests/modules/nf-core/tabix/bgziptabix/** tabix/tabix: - - modules/tabix/tabix/** - - tests/modules/tabix/tabix/** + - modules/nf-core/tabix/tabix/** + - tests/modules/nf-core/tabix/tabix/** tailfindr: - - modules/tailfindr/** - - tests/modules/tailfindr/** + - modules/nf-core/tailfindr/** + - tests/modules/nf-core/tailfindr/** tbprofiler/profile: - - modules/tbprofiler/profile/** - - tests/modules/tbprofiler/profile/** + - modules/nf-core/tbprofiler/profile/** + - tests/modules/nf-core/tbprofiler/profile/** tiddit/cov: - - modules/tiddit/cov/** - - tests/modules/tiddit/cov/** + - modules/nf-core/tiddit/cov/** + - tests/modules/nf-core/tiddit/cov/** tiddit/sv: - - modules/tiddit/sv/** - - tests/modules/tiddit/sv/** + - modules/nf-core/tiddit/sv/** + - tests/modules/nf-core/tiddit/sv/** transdecoder/longorf: - - modules/transdecoder/longorf/** - - tests/modules/transdecoder/longorf/** + - modules/nf-core/transdecoder/longorf/** + - tests/modules/nf-core/transdecoder/longorf/** transdecoder/predict: - - modules/transdecoder/predict/** - - tests/modules/transdecoder/predict/** + - modules/nf-core/transdecoder/predict/** + - tests/modules/nf-core/transdecoder/predict/** trimgalore: - - modules/trimgalore/** - - tests/modules/trimgalore/** + - modules/nf-core/trimgalore/** + - tests/modules/nf-core/trimgalore/** trimmomatic: - - modules/trimmomatic/** - - tests/modules/trimmomatic/** + - modules/nf-core/trimmomatic/** + - tests/modules/nf-core/trimmomatic/** ucsc/bedclip: - - modules/ucsc/bedclip/** - - tests/modules/ucsc/bedclip/** + - modules/nf-core/ucsc/bedclip/** + - tests/modules/nf-core/ucsc/bedclip/** ucsc/bedgraphtobigwig: - - modules/ucsc/bedgraphtobigwig/** - - tests/modules/ucsc/bedgraphtobigwig/** + - modules/nf-core/ucsc/bedgraphtobigwig/** + - tests/modules/nf-core/ucsc/bedgraphtobigwig/** ucsc/bedtobigbed: - - modules/ucsc/bedtobigbed/** - - tests/modules/ucsc/bedtobigbed/** + - modules/nf-core/ucsc/bedtobigbed/** + - tests/modules/nf-core/ucsc/bedtobigbed/** ucsc/bigwigaverageoverbed: - - modules/ucsc/bigwigaverageoverbed/** - - tests/modules/ucsc/bigwigaverageoverbed/** + - modules/nf-core/ucsc/bigwigaverageoverbed/** + - tests/modules/nf-core/ucsc/bigwigaverageoverbed/** ucsc/liftover: - - modules/ucsc/liftover/** - - tests/modules/ucsc/liftover/** + - modules/nf-core/ucsc/liftover/** + - tests/modules/nf-core/ucsc/liftover/** ucsc/wigtobigwig: - - modules/ucsc/wigtobigwig/** - - tests/modules/ucsc/wigtobigwig/** + - modules/nf-core/ucsc/wigtobigwig/** + - tests/modules/nf-core/ucsc/wigtobigwig/** ultra/align: - - modules/ultra/align/** - - tests/modules/ultra/align/** + - modules/nf-core/ultra/align/** + - tests/modules/nf-core/ultra/align/** ultra/index: - - modules/ultra/index/** - - tests/modules/ultra/index/** + - modules/nf-core/ultra/index/** + - tests/modules/nf-core/ultra/index/** ultra/pipeline: - - modules/ultra/pipeline/** - - tests/modules/ultra/pipeline/** + - modules/nf-core/ultra/pipeline/** + - tests/modules/nf-core/ultra/pipeline/** umitools/dedup: - - modules/umitools/dedup/** - - modules/umitools/extract/** - - tests/modules/umitools/dedup/** + - modules/nf-core/umitools/dedup/** + - modules/nf-core/umitools/extract/** + - tests/modules/nf-core/umitools/dedup/** umitools/extract: - - modules/umitools/extract/** - - tests/modules/umitools/extract/** + - modules/nf-core/umitools/extract/** + - tests/modules/nf-core/umitools/extract/** unicycler: - - modules/unicycler/** - - tests/modules/unicycler/** + - modules/nf-core/unicycler/** + - tests/modules/nf-core/unicycler/** untar: - - modules/untar/** - - tests/modules/untar/** + - modules/nf-core/untar/** + - tests/modules/nf-core/untar/** unzip: - - modules/unzip/** - - tests/modules/unzip/** + - modules/nf-core/unzip/** + - tests/modules/nf-core/unzip/** vardictjava: - - modules/vardictjava/** - - tests/modules/vardictjava/** + - modules/nf-core/vardictjava/** + - tests/modules/nf-core/vardictjava/** variantbam: - - modules/variantbam/** - - tests/modules/variantbam/** + - modules/nf-core/variantbam/** + - tests/modules/nf-core/variantbam/** vcf2db: - - modules/vcf2db/** - - tests/modules/vcf2db/** + - modules/nf-core/vcf2db/** + - tests/modules/nf-core/vcf2db/** vcf2maf: - - modules/vcf2maf/** - - tests/modules/vcf2maf/** + - modules/nf-core/vcf2maf/** + - tests/modules/nf-core/vcf2maf/** vcfanno: - - modules/vcfanno/** - - tests/modules/vcfanno/** + - modules/nf-core/vcfanno/** + - tests/modules/nf-core/vcfanno/** vcflib/vcfbreakmulti: - - modules/vcflib/vcfbreakmulti/** - - tests/modules/vcflib/vcfbreakmulti/** + - modules/nf-core/vcflib/vcfbreakmulti/** + - tests/modules/nf-core/vcflib/vcfbreakmulti/** vcflib/vcfuniq: - - modules/vcflib/vcfuniq/** - - tests/modules/vcflib/vcfuniq/** + - modules/nf-core/vcflib/vcfuniq/** + - tests/modules/nf-core/vcflib/vcfuniq/** vcftools: - - modules/vcftools/** - - tests/modules/vcftools/** + - modules/nf-core/vcftools/** + - tests/modules/nf-core/vcftools/** vsearch/sintax: - - modules/vsearch/sintax/** - - tests/modules/vsearch/sintax/** + - modules/nf-core/vsearch/sintax/** + - tests/modules/nf-core/vsearch/sintax/** vsearch/usearchglobal: - - modules/vsearch/usearchglobal/** - - tests/modules/vsearch/usearchglobal/** + - modules/nf-core/vsearch/usearchglobal/** + - tests/modules/nf-core/vsearch/usearchglobal/** whamg: - - modules/whamg/** - - tests/modules/whamg/** + - modules/nf-core/whamg/** + - tests/modules/nf-core/whamg/** yara/index: - - modules/yara/index/** - - tests/modules/yara/index/** + - modules/nf-core/yara/index/** + - tests/modules/nf-core/yara/index/** yara/mapper: - - modules/yara/mapper/** - - tests/modules/yara/mapper/** + - modules/nf-core/yara/mapper/** + - tests/modules/nf-core/yara/mapper/**