Lint modules ci (#389)

* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

.github/workflows/pytest-workflow.yml

@@ -40,6 +40,20 @@ jobs:
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+        # FIXME: Remove this when nf-core modules lint stabilizes
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint . -t ${{ matrix.tags }}
+
       - uses: actions/cache@v2
         with:
           path: /usr/local/bin/nextflow
@@ -54,12 +68,6 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: python -m pip install --upgrade pip pytest-workflow
 
       - name: Set up Singularity
         if: matrix.profile == 'singularity'

tests/config/pytest_software.yml

@@ -6,85 +6,85 @@ allelecounter:
   - software/allelecounter/**
   - tests/software/allelecounter/**
 
-bandage_image:
+bandage/image:
   - software/bandage/image/**
   - tests/software/bandage/image/**
 
-bcftools_consensus:
+bcftools/consensus:
   - software/bcftools/consensus/**
   - tests/software/bcftools/consensus/**
 
-bcftools_filter:
+bcftools/filter:
   - software/bcftools/filter/**
   - tests/software/bcftools/filter/**
 
-bcftools_isec:
+bcftools/isec:
   - software/bcftools/isec/**
   - tests/software/bcftools/isec/**
 
-bcftools_merge:
+bcftools/merge:
   - software/bcftools/merge/**
   - tests/software/bcftools/merge/**
 
-bcftools_mpileup:
+bcftools/mpileup:
   - software/bcftools/mpileup/**
   - tests/software/bcftools/mpileup/**
 
-bcftools_stats:
+bcftools/stats:
   - software/bcftools/stats/**
   - tests/software/bcftools/stats/**
 
-bedtools_complement:
+bedtools/complement:
   - software/bedtools/complement/**
   - tests/software/bedtools/complement/**
 
-bedtools_genomecov:
+bedtools/genomecov:
   - software/bedtools/genomecov/**
   - tests/software/bedtools/genomecov/**
 
-bedtools_getfasta:
+bedtools/getfasta:
   - software/bedtools/getfasta/**
   - tests/software/bedtools/getfasta/**
 
-bedtools_intersect:
+bedtools/intersect:
   - software/bedtools/intersect/**
   - tests/software/bedtools/intersect/**
 
-bedtools_maskfasta:
+bedtools/maskfasta:
   - software/bedtools/maskfasta/**
   - tests/software/bedtools/maskfasta/**
 
-bedtools_merge:
+bedtools/merge:
   - software/bedtools/merge/**
   - tests/software/bedtools/merge/**
 
-bedtools_slop:
+bedtools/slop:
   - software/bedtools/slop/**
   - tests/software/bedtools/slop/**
 
-bedtools_sort:
+bedtools/sort:
   - software/bedtools/sort/**
   - tests/software/bedtools/sort/**
 
-bismark_align:
+bismark/align:
   - software/bismark/align/**
   - software/bismark/genomepreparation/**
   - tests/software/bismark/align/**
 
-bismark_deduplicate:
+bismark/deduplicate:
   - software/bismark/deduplicate/**
   - tests/software/bismark/deduplicate/**
 
-bismark_genomepreparation:
+bismark/genomepreparation:
   - software/bismark/genomepreparation/**
   - tests/software/bismark/genomepreparation/**
 
-bismark_methylationextractor:
+bismark/methylationextractor:
   - software/bismark/methylationextractor/**
   - software/bismark/genomepreparation/**
   - tests/software/bismark/methylationextractor/**
 
-bismark_report:
+bismark/report:
   - software/bismark/genomepreparation/**
   - software/bismark/align/**
   - software/bismark/deduplicate/**
@@ -92,7 +92,7 @@ bismark_report:
   - software/bismark/report/**
   - tests/software/bismark/report/**
 
-bismark_summary:
+bismark/summary:
   - software/bismark/genomepreparation/**
   - software/bismark/align/**
   - software/bismark/deduplicate/**
@@ -100,57 +100,57 @@ bismark_summary:
   - software/bismark/summary/**
   - tests/software/bismark/summary/**
 
-blast_blastn:
+blast/blastn:
   - software/blast/blastn/**
   - tests/software/blast/blastn/**
 
-blast_makeblastdb:
+blast/makeblastdb:
   - software/blast/makeblastdb/**
   - tests/software/blast/makeblastdb/**
 
-bowtie2_align:
+bowtie2/align:
   - software/bowtie2/align/**
   - software/bowtie2/build/**
   - tests/software/bowtie2/align/**
 
-bowtie2_build:
+bowtie2/build:
   - software/bowtie2/build/**
   - tests/software/bowtie2/build_test/**
 
-bowtie_align:
+bowtie/align:
   - software/bowtie/align/**
   - software/bowtie/build/**
   - tests/software/bowtie/align/**
 
-bowtie_build:
+bowtie/build:
   - software/bowtie/build/**
   - tests/software/bowtie/build_test/**
 
-bwa_index:
+bwa/index:
   - software/bwa/index/**
   - tests/software/bwa/index/**
 
-bwa_mem:
+bwa/mem:
   - software/bwa/mem/**
   - tests/software/bwa/mem/**
 
-bwamem2_index:
+bwamem2/index:
   - software/bwamem2/index/**
   - tests/software/bwamem2/index/**
 
-bwamem2_mem:
+bwamem2/mem:
   - software/bwamem2/mem/**
   - tests/software/bwamem2/mem/**
 
-bwameth_align:
+bwameth/align:
   - software/bwameth/align/**
   - tests/software/bwameth/align/**
 
-bwameth_index:
+bwameth/index:
   - software/bwameth/index/**
   - tests/software/bwameth/index/**
 
-cat_fastq:
+cat/fastq:
   - software/cat/fastq/**
   - tests/software/cat/fastq/**
 
@@ -162,11 +162,11 @@ cutadapt:
   - software/cutadapt/**
   - tests/software/cutadapt/**
 
-dsh_filterbed:
+dsh/filterbed:
   - software/dsh/filterbed/**
   - tests/software/dsh/filterbed/**
 
-dsh_splitbed:
+dsh/splitbed:
   - software/dsh/splitbed/**
   - tests/software/dsh/splitbed/**
 
@@ -190,55 +190,55 @@ flash:
   - software/flash/**
   - tests/software/flash/**
 
-gatk4_applybqsr:
+gatk4/applybqsr:
   - software/gatk4/applybqsr/**
   - tests/software/gatk4/applybqsr/**
 
-gatk4_baserecalibrator:
+gatk4/baserecalibrator:
   - software/gatk4/baserecalibrator/**
   - tests/software/gatk4/baserecalibrator/**
 
-gatk4_bedtointervallist:
+gatk4/bedtointervallist:
   - software/gatk4/bedtointervallist/**
   - tests/software/gatk4/bedtointervallist/**
 
-gatk4_createsequencedictionary:
+gatk4/createsequencedictionary:
   - software/gatk4/createsequencedictionary/**
   - tests/software/gatk4/createsequencedictionary/**
 
-gatk4_fastqtosam:
+gatk4/fastqtosam:
   - software/gatk4/fastqtosam/**
   - tests/software/gatk4/fastqtosam/**
 
-gatk4_haplotypecaller:
+gatk4/haplotypecaller:
   - software/gatk4/haplotypecaller/**
   - tests/software/gatk4/haplotypecaller/**
 
-gatk4_markduplicates:
+gatk4/markduplicates:
   - software/gatk4/markduplicates/**
   - tests/software/gatk4/markduplicates/**
 
-gatk4_mergebamalignment:
+gatk4/mergebamalignment:
   - software/gatk4/mergebamalignment/**
   - tests/software/gatk4/mergebamalignment/**
 
-gatk4_mergevcfs:
+gatk4/mergevcfs:
   - software/gatk4/mergevcfs/**
   - tests/software/gatk4/mergevcfs/**
 
-gatk4_revertsam:
+gatk4/revertsam:
   - software/gatk4/revertsam/**
   - tests/software/gatk4/revertsam/**
 
-gatk4_samtofastq:
+gatk4/samtofastq:
   - software/gatk4/samtofastq/**
   - tests/software/gatk4/samtofastq/**
 
-gatk4_splitncigarreads:
+gatk4/splitncigarreads:
   - software/gatk4/splitncigarreads/**
   - tests/software/gatk4/splitncigarreads/**
 
-gatk4_variantfiltration:
+gatk4/variantfiltration:
   - software/gatk4/variantfiltration/**
   - tests/software/gatk4/variantfiltration/**
 
@@ -254,50 +254,50 @@ gunzip:
   - software/gunzip/**
   - tests/software/gunzip/**
 
-hisat2_align:
+hisat2/align:
   - software/hisat2/align/**
   - software/hisat2/build/**
   - software/hisat2/extractsplicesites/**
   - tests/software/hisat2/align/**
 
-hisat2_build:
+hisat2/build:
   - software/hisat2/build/**
   - software/hisat2/extractsplicesites/**
   - tests/software/hisat2/build_test/**
 
-hisat2_extractsplicesites:
+hisat2/extractsplicesites:
   - software/hisat2/extractsplicesites/**
   - tests/software/hisat2/extractsplicesites/**
 
-homer_annotatepeaks:
+homer/annotatepeaks:
   - software/homer/annotatepeaks/**
   - tests/software/homer/annotatepeaks/**
 
-ivar_consensus:
+ivar/consensus:
   - software/ivar/consensus/**
   - tests/software/ivar/consensus/**
 
-ivar_trim:
+ivar/trim:
   - software/ivar/trim/**
   - tests/software/ivar/trim/**
 
-ivar_variants:
+ivar/variants:
   - software/ivar/variants/**
   - tests/software/ivar/variants/**
 
-kallisto_index:
+kallisto/index:
   - software/kallisto/index/**
   - tests/software/kallisto/index/**
 
-kraken2_run:
+kraken2/run:
   - software/kraken2/run/**
   - tests/software/kraken2/run/**
 
-methyldackel_extract:
+methyldackel/extract:
   - software/methyldackel/extract/**
   - tests/software/methyldackel/extract/**
 
-methyldackel_mbias:
+methyldackel/mbias:
   - software/methyldackel/mbias/**
   - tests/software/methyldackel/mbias/**
 
@@ -305,7 +305,7 @@ minia:
   - software/minia/**
   - tests/software/minia/**
 
-minimap2_align:
+minimap2/align:
   - software/minimap2/align/**
   - tests/software/minimap2/align/**
 
@@ -334,23 +334,23 @@ pangolin:
   - software/pangolin/**
   - tests/software/pangolin/**
 
-picard_collectmultiplemetrics:
+picard/collectmultiplemetrics:
   - software/picard/collectmultiplemetrics/**
   - tests/software/picard/collectmultiplemetrics/**
 
-picard_collectwgsmetrics:
+picard/collectwgsmetrics:
   - software/picard/collectwgsmetrics/**
   - tests/software/picard/collectwgsmetrics/**
 
-picard_markduplicates:
+picard/markduplicates:
   - software/picard/markduplicates/**
   - tests/software/picard/markduplicates/**
 
-picard_mergesamfiles:
+picard/mergesamfiles:
   - software/picard/mergesamfiles/**
   - tests/software/picard/mergesamfiles/**
 
-preseq_lcextrap:
+preseq/lcextrap:
   - software/preseq/lcextrap/**
   - tests/software/preseq/lcextrap/**
 
@@ -362,7 +362,7 @@ prokka:
   - software/prokka/**
   - tests/software/prokka/**
 
-qualimap_bamqc:
+qualimap/bamqc:
   - software/qualimap/bamqc/**
   - tests/software/qualimap/bamqc/**
 
@@ -370,79 +370,79 @@ quast:
   - software/quast/**
   - tests/software/quast/**
 
-salmon_index:
+salmon/index:
   - software/salmon/index/**
   - tests/software/salmon/index/**
 
-salmon_quant:
+salmon/quant:
   - software/salmon/quant/**
   - tests/software/salmon/quant/**
 
-samtools_faidx:
+samtools/faidx:
   - software/samtools/faidx/**
   - tests/software/samtools/faidx/**
 
-samtools_fastq:
+samtools/fastq:
   - software/samtools/fastq/**
   - tests/software/samtools/fastq/**
 
-samtools_flagstat:
+samtools/flagstat:
   - software/samtools/flagstat/**
   - tests/software/samtools/flagstat/**
 
-samtools_idxstats:
+samtools/idxstats:
   - software/samtools/idxstats/**
   - tests/software/samtools/idxstats/**
 
-samtools_index:
+samtools/index:
   - software/samtools/index/**
   - tests/software/samtools/index/**
 
-samtools_merge:
+samtools/merge:
   - software/samtools/merge/**
   - tests/software/samtools/merge/**
 
-samtools_mpileup:
+samtools/mpileup:
   - software/samtools/mpileup/**
   - tests/software/samtools/mpileup/**
 
-samtools_sort:
+samtools/sort:
   - software/samtools/sort/**
   - tests/software/samtools/sort/**
 
-samtools_stats:
+samtools/stats:
   - software/samtools/stats/**
   - tests/software/samtools/stats/**
 
-samtools_view:
+samtools/view:
   - software/samtools/view/**
   - tests/software/samtools/view/**
 
-seacr_callpeak:
+seacr/callpeak:
   - software/seacr/callpeak/**
   - tests/software/seacr/callpeak/**
 
-seqkit_split2:
+seqkit/split2:
   - software/seqkit/split2/**
   - tests/software/seqkit/split2/**
 
-sequenza_bam2seqz:
+sequenza/bam2seqz:
   - software/sequenza/bam2seqz/**
   - tests/software/sequenza/bam2seqz/**
 
-sequenza_wiggle:
+sequenza/wiggle:
   - software/sequenza/wiggle/**
   - tests/software/sequenza/wiggle/**
 
-sequenzautils_bam2seqz:
+sequenzautils/bam2seqz:
   - software/sequenzautils/bam2seqz/**
   - tests/software/sequenzautils/bam2seqz/**
 
-sequenzautils_gcwiggle:
+sequenzautils/gcwiggle:
   - software/sequenzautils/gcwiggle/**
   - tests/software/sequenzautils/gcwiggle/**
 
-seqwish_induce:
+seqwish/induce:
   - software/seqwish/induce/**
   - tests/software/seqwish/induce/**
 
@@ -454,15 +454,15 @@ spades:
   - software/spades/**
   - tests/software/spades/**
 
-star_align:
+star/align:
   - software/star/align/**
   - tests/software/star/align/**
 
-star_genomegenerate:
+star/genomegenerate:
   - software/star/genomegenerate/**
   - tests/software/star/genomegenerate/**
 
-strelka_germline:
+strelka/germline:
   - software/strelka/germline/**
   - tests/software/strelka/germline/**
 
@@ -470,19 +470,19 @@ stringtie:
   - software/stringtie/**
   - tests/software/stringtie/**
 
-subread_featurecounts:
+subread/featurecounts:
   - software/subread/featurecounts/**
   - tests/software/subread/featurecounts/**
 
-tabix_bgzip:
+tabix/bgzip:
   - software/tabix/bgzip/**
   - tests/software/tabix/bgzip/**
 
-tabix_tabix:
+tabix/tabix:
   - software/tabix/tabix/**
   - tests/software/tabix/tabix/**
 
-tiddit_sv:
+tiddit/sv:
   - software/tiddit/sv/**
   - tests/software/tiddit/sv/**
 
@@ -490,11 +490,11 @@ trimgalore:
   - software/trimgalore/**
   - tests/software/trimgalore/**
 
-ucsc_bed12tobigbed:
+ucsc/bed12tobigbed:
   - software/ucsc/bed12tobigbed/**
   - tests/software/ucsc/bed12tobigbed/**
 
-ucsc_bedgraphtobigwig:
+ucsc/bedgraphtobigwig:
   - software/ucsc/bedgraphtobigwig/**
   - tests/software/ucsc/bedgraphtobigwig/**
 
@@ -514,6 +514,6 @@ yara:
   - software/yara/mapper/**
   - tests/software/yara/mapper/**
 
-yara_index:
+yara/index:
   - software/yara/index/**
   - tests/software/yara/index/**

tests/software/bandage/image/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bandage/image -entry test_bandage_image -c tests/config/nextflow.config
   tags:
     - bandage
-    - bandage_image
+    - bandage/image
   files:
     - path: output/bandage/B-3106.png
     - path: output/bandage/B-3106.svg

tests/software/bcftools/consensus/test.yml

@@ -1,7 +1,7 @@
 - name: bcftools consensus test_bcftools_consensus
   command: nextflow run tests/software/bcftools/consensus -entry test_bcftools_consensus -c tests/config/nextflow.config
   tags:
-    - bcftools_consensus
+    - bcftools/consensus
     - bcftools
   files:
     - path: output/bcftools/test.fa

tests/software/bcftools/filter/test.yml

@@ -1,7 +1,7 @@
 - name: bcftools filter test_bcftools_filter
   command: nextflow run tests/software/bcftools/filter -entry test_bcftools_filter -c tests/config/nextflow.config
   tags:
-    - bcftools_filter
+    - bcftools/filter
     - bcftools
   files:
     - path: output/bcftools/test.vcf.gz

tests/software/bcftools/isec/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/bcftools/isec -entry test_bcftools_isec -c tests/config/nextflow.config
   tags:
     - bcftools
-    - bcftools_isec
+    - bcftools/isec
   files:
     - path: output/bcftools/test/0000.vcf.gz
       md5sum: fc178eb342a91dc0d1d568601ad8f8e2

tests/software/bcftools/merge/test.yml

@@ -1,7 +1,7 @@
 - name: bcftools merge test_bcftools_merge
   command: nextflow run tests/software/bcftools/merge -entry test_bcftools_merge -c tests/config/nextflow.config
   tags:
-    - bcftools_merge
+    - bcftools/merge
     - bcftools
   files:
     - path: output/bcftools/test.vcf.gz

tests/software/bcftools/mpileup/test.yml

@@ -1,7 +1,7 @@
 - name: bcftools mpileup test_bcftools_mpileup
   command: nextflow run tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
   tags:
-    - bcftools_mpileup
+    - bcftools/mpileup
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt

tests/software/bcftools/stats/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/bcftools/stats -entry test_bcftools_stats -c tests/config/nextflow.config
   tags:
     - bcftools
-    - bcftools_stats
+    - bcftools/stats
   files:
     - path: output/bcftools/test.bcftools_stats.txt
       md5sum: c4c5938add12a20050eec3782c8ad623

tests/software/bedtools/complement/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/complement -entry test_bedtools_complement -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_complement
+    - bedtools/complement
   files:
     - path: ./output/bedtools/test_out.bed
       md5sum: d71df7e47aec0661c27b71e483e727f9

tests/software/bedtools/genomecov/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_genomecov
+    - bedtools/genomecov
   files:
     - path: ./output/bedtools/test_out.bed
       md5sum: 66083198daca6c001d328ba9616e9b53

tests/software/bedtools/getfasta/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/getfasta -entry test_bedtools_getfasta -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_getfasta
+    - bedtools/getfasta
   files:
     - path: ./output/bedtools/test.fa
       md5sum: 41c3a45a57a16c04f828d8f8bb52df70

tests/software/bedtools/intersect/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_intersect
+    - bedtools/intersect
   files:
     - path: ./output/bedtools/test_out.bed
       md5sum: d41d8cd98f00b204e9800998ecf8427e

tests/software/bedtools/maskfasta/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/maskfasta -entry test_bedtools_maskfasta -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_maskfasta
+    - bedtools/maskfasta
   files:
     - path: ./output/bedtools/test.fa
       md5sum: f4f6749698f11074228d2c79338e3b9c

tests/software/bedtools/merge/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/merge -entry test_bedtools_merge -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_merge
+    - bedtools/merge
   files:
     - path: ./output/bedtools/test_out.bed
       md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e

tests/software/bedtools/slop/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/slop -entry test_bedtools_slop -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_slop
+    - bedtools/slop
   files:
     - path: ./output/bedtools/test_out.bed
       md5sum: 4f1d8924925fe5d205c9e1981fe290a4

tests/software/bedtools/sort/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bedtools/sort -entry test_bedtools_sort -c tests/config/nextflow.config
   tags:
     - bedtools
-    - bedtools_sort
+    - bedtools/sort
   files:
     - path: ./output/bedtools/test_out.bed
       md5sum: fe4053cf4de3aebbdfc3be2efb125a74

tests/software/bismark/align/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_align
+    - bismark/align
   files:
     - path: output/test_single_end/test_methylated_1_bismark_bt2.bam
       md5sum: 7f9744cec5aa7908675e5fae79af36fc
@@ -12,7 +12,7 @@
   command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_align
+    - bismark/align
   files:
     - path: output/test_paired_end/test_methylated_1_bismark_bt2_pe.bam
       md5sum: b13d0d40dffd336375f80fc94acc295f

tests/software/bismark/deduplicate/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_deduplicate
+    - bismark/deduplicate
   files:
     - path: output/bismark/test_methylated_paired_end.deduplicated.bam
     - path: output/bismark/test_methylated_paired_end.deduplication_report.txt

tests/software/bismark/genomepreparation/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_genomepreparation
+    - bismark/genomepreparation
   files:
     - path: ./output/bismark/BismarkIndex/genome.fasta
       md5sum: 6e9fe4042a72f2345f644f239272b7e6

tests/software/bismark/methylationextractor/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_methylationextractor
+    - bismark/methylationextractor
   files:
     - path: output/bismark/CHG_OB_test_methylated_paired_end.txt.gz
     - path: output/bismark/CHG_OT_test_methylated_paired_end.txt.gz

tests/software/bismark/report/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bismark/report -entry test_bismark_report -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_report
+    - bismark/report
   files:
     - path: output/bismark/test_methylated_1_bismark_bt2_PE_report.txt
     - path: output/bismark/test_methylated_1_bismark_bt2_PE_report.html

tests/software/bismark/summary/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bismark/summary -entry test_bismark_summary -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_summary
+    - bismark/summary
   files:
     - path: output/bismark/bismark_summary_report.html
     - path: output/bismark/bismark_summary_report.txt

tests/software/blast/blastn/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/blast/blastn -entry test_blast_blastn -c tests/config/nextflow.config
   tags:
     - blast
-    - blast_blastn
+    - blast/blastn
   files:
     - path: ./output/blast/test.blastn.txt
     - path: ./output/blast/blast_db/genome.fasta.nsq

tests/software/blast/makeblastdb/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/blast/makeblastdb -entry test_blast_makeblastdb -c tests/config/nextflow.config
   tags:
     - blast
-    - blast_makeblastdb
+    - blast/makeblastdb
   files:
     - path: ./output/blast/blast_db/genome.fasta.nsq
       md5sum: 982cbc7d9e38743b9b1037588862b9da

tests/software/bowtie/align/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bowtie_align
+    - bowtie/align
     - bowtie_align_single_end
   files:
     - path: ./output/bowtie/test.bam
@@ -25,7 +25,7 @@
   command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bowtie_align
+    - bowtie/align
     - bowtie_align_paired_end
   files:
     - path: ./output/bowtie/test.bam

tests/software/bowtie/build_test/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bowtie/build_test -entry test_bowtie_build -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bowtie_build
+    - bowtie/build
   files:
     - path: ./output/index/bowtie/test_genome.3.ebwt
       md5sum: 4ed93abba181d8dfab2e303e33114777

tests/software/bowtie2/align/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
   tags:
     - bowtie2
-    - bowtie2_align
+    - bowtie2/align
     - bowtie2_align_single_end
   files:
     - path: ./output/bowtie2/test.bam
@@ -24,7 +24,7 @@
   command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie2
-    - bowtie2_align
+    - bowtie2/align
     - bowtie2_align_paired_end
   files:
     - path: ./output/bowtie2/test.bam

tests/software/bowtie2/build_test/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bowtie2/build_test -entry test_bowtie2_build -c tests/config/nextflow.config
   tags:
     - bowtie2
-    - bowtie2_build
+    - bowtie2/build
   files:
     - path: ./output/index/bowtie2/genome.3.bt2
       md5sum: 4ed93abba181d8dfab2e303e33114777

tests/software/bwa/index/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
   tags:
     - bwa
-    - bwa_index
+    - bwa/index
   files:
     - path: ./output/index/bwa/genome.bwt
       md5sum: 0469c30a1e239dd08f68afe66fde99da

tests/software/bwa/mem/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
   tags:
     - bwa
-    - bwa_mem
+    - bwa/mem
     - bwa_mem_single_end
   files:
     - path: ./output/bwa/test.bam
@@ -22,7 +22,7 @@
   command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
   tags:
     - bwa
-    - bwa_mem
+    - bwa/mem
     - bwa_mem_paired_end
   files:
     - path: ./output/bwa/test.bam

tests/software/bwamem2/index/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bwamem2/index -entry test_bwamem2_index -c tests/config/nextflow.config
   tags:
     - bwamem2
-    - bwamem2_index
+    - bwamem2/index
   files:
     - path: ./output/index/bwamem2/genome.fasta.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e

tests/software/bwamem2/mem/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_single_end -c tests/config/nextflow.config
   tags:
     - bwamem2
-    - bwamem2_mem
+    - bwamem2/mem
     - bwamem2_mem_single_end
   files:
     - path: ./output/bwamem2/test.bam
@@ -22,7 +22,7 @@
   command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_paired_end -c tests/config/nextflow.config
   tags:
     - bwamem2
-    - bwamem2_mem
+    - bwamem2/mem
     - bwamem2_mem_paired_end
   files:
     - path: ./output/bwamem2/test.bam

tests/software/bwameth/align/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_single_end -c tests/config/nextflow.config
   tags:
     - bwameth
-    - bwameth_align
+    - bwameth/align
   files:
     - path: output/test_single_end/test.bam
 
@@ -10,7 +10,7 @@
   command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
   tags:
     - bwameth
-    - bwameth_align
+    - bwameth/align
   files:
     - path: output/test_paired_end/test.bam
 

tests/software/bwameth/index/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
   tags:
     - bwameth
-    - bwameth_index
+    - bwameth/index
   files:
     - path: ./output/index/bwameth/genome.fasta.bwameth.c2t
       md5sum: 98039984526a41d04d6bd92fcc040c62

tests/software/cat/fastq/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_single_end -c tests/config/nextflow.config
   tags:
     - cat
-    - cat_fastq
+    - cat/fastq
     - cat_fastqc_single_end
   files:
     - path: ./output/merged_fastq/test.merged.fastq.gz
@@ -12,7 +12,7 @@
   command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config
   tags:
     - cat
-    - cat_fastq
+    - cat/fastq
     - cat_fastqc_paired_end
   files:
     - path: ./output/merged_fastq/test_2.merged.fastq.gz

tests/software/dsh/filterbed/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/dsh/filterbed -entry test_dsh_filterbed -c tests/config/nextflow.config
   tags:
     - dsh
-    - dsh_filterbed
+    - dsh/filterbed
   files:
     - path: ./output/dsh/test.filtered.bed.gz
       md5sum: 163be0a88c70ca629fd516dbaadad96a

tests/software/dsh/splitbed/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/dsh/splitbed -entry test_dsh_splitbed -c tests/config/nextflow.config
   tags:
     - dsh
-    - dsh_splitbed
+    - dsh/splitbed
   files:
     - path: ./output/dsh/test.1.bed.gz
       md5sum: 967ba338f361740eb015304003ababe7

tests/software/gatk4/applybqsr/test.yml

@@ -1,8 +1,8 @@
 - name: gatk4 applybqsr test_gatk4_applybqsr
   command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config
   tags:
-    - gatk4_applybqsr
     - gatk4
+    - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
       md5sum: 139a5ffc7601ce3cfa7a896cd381542a
@@ -10,9 +10,9 @@
 - name: gatk4 applybqsr test_gatk4_applybqsr_intervals
   command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
   tags:
-    - gatk4_applybqsr
-    - gatk4_applybqsr_intervals
     - gatk4
+    - gatk4/applybqsr/intervals
+    - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
       md5sum: 5b1f6fa2525124c281f71e5a76d28482

tests/software/gatk4/baserecalibrator/test.yml

@@ -1,7 +1,7 @@
 - name: gatk4 baserecalibrator test_gatk4_baserecalibrator
   command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c tests/config/nextflow.config
   tags:
-    - gatk4_baserecalibrator
+    - gatk4/baserecalibrator
     - gatk4
   files:
     - path: output/gatk4/test.table
@@ -10,8 +10,8 @@
 - name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
   command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
   tags:
-    - gatk4_baserecalibrator_intervals
+    - gatk4/baserecalibrator/intervals
-    - gatk4_baserecalibrator
+    - gatk4/baserecalibrator
     - gatk4
   files:
     - path: output/gatk4/test.table
@@ -21,7 +21,7 @@
   command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
   tags:
     - gatk4_baserecalibrator_multiple_sites
-    - gatk4_baserecalibrator
+    - gatk4/baserecalibrator
     - gatk4
   files:
     - path: output/gatk4/test.table

tests/software/gatk4/bedtointervallist/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_bedtointervallist
+    - gatk4/bedtointervallist
   files:
     - path: output/gatk4/test.interval_list
       md5sum: e51101c9357fb2d59fd30e370eefa39c

tests/software/gatk4/fastqtosam/test.yml

@@ -2,8 +2,8 @@
   command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
   tags:
     - gatk4_fastqtosam_single_end
+    - gatk4/fastqtosam
     - gatk4
-    - gatk4_fastqtosam
   files:
     - path: output/gatk4/test.bam
       md5sum: 4967100b2e4912c0e4ce0976d946bafb
@@ -13,7 +13,7 @@
   tags:
     - gatk4_fastqtosam_paired_end
     - gatk4
-    - gatk4_fastqtosam
+    - gatk4/fastqtosam
   files:
     - path: output/gatk4/test.bam
       md5sum: 4967100b2e4912c0e4ce0976d946bafb

tests/software/gatk4/mergebamalignment/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_mergebamalignment
+    - gatk4/mergebamalignment
   files:
     - path: output/gatk4/test.merged.bam
       md5sum: bd4a5e2ea916826aadebb5878333e26f

tests/software/gatk4/mergevcfs/test.yml

@@ -1,7 +1,7 @@
 - name: gatk4 mergevcfs test_gatk4_mergevcfs
   command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
   tags:
-    - gatk4_mergevcfs
+    - gatk4/mergevcfs
     - gatk4
   files:
     - path: output/gatk4/test.merged.vcf.gz
@@ -10,9 +10,9 @@
 - name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict
   command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
   tags:
-    - gatk4_mergevcfs
+    - gatk4/mergevcfs
     - gatk4
-    - gatk4_mergevcfs_refdict
+    - gatk4/mergevcfs_refdict
   files:
     - path: output/gatk4/test.merged.vcf.gz
       md5sum: ff48f175e26db2d4b2957762f6d1c715

tests/software/gatk4/revertsam/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_revertsam
+    - gatk4/revertsam
   files:
     - path: output/gatk4/test.reverted.bam
       md5sum: f778310b18b83b49929eb648594f96dc

tests/software/gatk4/samtofastq/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_samtofastq
+    - gatk4/samtofastq
     - gatk4_samtofastq_single_end
   files:
     - path: output/gatk4/test.fastq.gz
@@ -12,7 +12,7 @@
   command: nextflow run tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_samtofastq
+    - gatk4/samtofastq
     - gatk4_samtofastq_paired_end
   files:
     - path: output/gatk4/test_1.fastq.gz

tests/software/gatk4/splitncigarreads/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4_splitncigarreads
+    - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.split_cigar.bam
       md5sum: a8473bd4abc7b13751fc51b92531da4c

tests/software/gatk4/variantfiltration/test.yml

@@ -1,7 +1,7 @@
 - name: gatk4 variantfiltration test_gatk4_variantfiltration
   command: nextflow run tests/software/gatk4/variantfiltration -entry test_gatk4_variantfiltration -c tests/config/nextflow.config
   tags:
-    - gatk4_variantfiltration
+    - gatk4/variantfiltration
     - gatk4
   files:
     - path: output/gatk4/test.filtered.vcf

tests/software/homer/annotatepeaks/test.yml

@@ -2,6 +2,6 @@
   command: nextflow run tests/software/homer/annotatepeaks -entry test_homer_annotatepeaks -c tests/config/nextflow.config
   tags:
     - homer
-    - homer_annotatepeaks
+    - homer/annotatepeaks
   files:
     - path: output/homer/test.annotatePeaks.txt

tests/software/ivar/consensus/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/ivar/consensus -entry test_ivar_consensus -c tests/config/nextflow.config
   tags:
     - ivar
-    - ivar_consensus
+    - ivar/consensus
   files:
     - path: output/ivar/test.fa
       md5sum: 9e21a64818f4302b4dece5480fa5e8b8

tests/software/ivar/trim/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/ivar/trim -entry test_ivar_trim -c tests/config/nextflow.config
   tags:
     - ivar
-    - ivar_trim
+    - ivar/trim
   files:
     - path: output/ivar/test.bam
       md5sum: 8705d032b28a1c3dbfe78fa762a2132f

tests/software/ivar/variants/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c tests/config/nextflow.config
   tags:
     - ivar
-    - ivar_variants
+    - ivar/variants
   files:
     - path: output/ivar/test.tsv
       md5sum: 728f1430f2402861396d9953465ac706
@@ -11,7 +11,7 @@
   command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config --save_mpileup
   tags:
     - ivar
-    - ivar_variants
+    - ivar/variants
   files:
     - path: output/ivar/test.tsv
       md5sum: 728f1430f2402861396d9953465ac706
@@ -22,7 +22,7 @@
   command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup
   tags:
     - ivar
-    - ivar_variants
+    - ivar/variants
   files:
     - path: output/ivar/test.tsv
       md5sum: 7b59146132a60da58444bebffc3c2577

tests/software/kallisto/index/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/kallisto/index -entry test_kallisto_index -c tests/config/nextflow.config
   tags:
     - kallisto
-    - kallisto_index
+    - kallisto/index
   files:
     - path: output/kallisto/kallisto
       md5sum: bf8a58d329dddc96f0c32f7823bc0310

tests/software/kraken2/run/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/kraken2/run -entry test_kraken2_run_single_end -c tests/config/nextflow.config
   tags:
     - kraken2
-    - kraken2_run
+    - kraken2/run
     - kraken2_run_single_end
   files:
     - path: output/kraken2/test.classified.fastq.gz
@@ -16,7 +16,7 @@
   command: nextflow run ./tests/software/kraken2/run -entry test_kraken2_run_paired_end -c tests/config/nextflow.config
   tags:
     - kraken2
-    - kraken2_run
+    - kraken2/run
     - kraken2_run_paired_end
   files:
     - path: output/kraken2/test.classified_1.fastq.gz

tests/software/methyldackel/extract/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
   tags:
     - methyldackel
-    - methyldackel_extract
+    - methyldackel/extract
   files:
     - path: output/methyldackel/test_methylated_paired_end.sorted_CpG.bedGraph
       md5sum: d7c637e2ef20de401fc610206f6bf6b7

tests/software/methyldackel/mbias/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
   tags:
     - methyldackel
-    - methyldackel_mbias
+    - methyldackel/mbias
   files:
     - path: output/methyldackel/test.mbias.txt
       md5sum: 357bb944dc2cdffcc47fa0d34376e016

tests/software/minimap2/align/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
   tags:
     - minimap2
-    - minimap2_align
+    - minimap2/align
     - minimap2_align_single_end
   files:
     - path: ./output/minimap2/test.paf
@@ -12,7 +12,7 @@
   command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
   tags:
     - minimap2
-    - minimap2_align
+    - minimap2/align
     - minimap2_align_paired_end
   files:
     - path: ./output/minimap2/test.paf

tests/software/picard/collectwgsmetrics/test.yml

@@ -1,7 +1,7 @@
 - name: picard collectwgsmetrics test_picard_collectwgsmetrics
   command: nextflow run tests/software/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c tests/config/nextflow.config
   tags:
-    - picard_collectwgsmetrics
+    - picard/collectwgsmetrics
     - picard
   files:
     - path: output/picard/test.CollectWgsMetrics.coverage_metrics

tests/software/picard/markduplicates/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
   tags:
     - picard
-    - picard_markduplicates
+    - picard/markduplicates
   files:
     - path: ./output/picard/test.MarkDuplicates.metrics.txt
     - path: ./output/picard/test.bam
@@ -12,6 +12,6 @@
   command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
   tags:
     - picard
-    - picard_markduplicates
+    - picard/markduplicates
     - should fail
   exit_code: 1

tests/software/picard/mergesamfiles/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config
   tags:
     - picard
-    - picard_mergesamfiles
+    - picard/mergesamfiles
   files:
     - path: ./output/picard/test.bam
       md5sum: b8bd6c22f36c6ebc91bca98bd637a2eb

tests/software/preseq/lcextrap/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config
   tags:
     - preseq
-    - preseq_lcextrap
+    - preseq/lcextrap
     - preseq_lcextrap_single_end
   files:
     - path: output/preseq/test.ccurve.txt
@@ -13,7 +13,7 @@
   command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config
   tags:
     - preseq
-    - preseq_lcextrap
+    - preseq/lcextrap
     - preseq_lcextrap_paired_end
   files:
     - path: output/preseq/test.ccurve.txt

tests/software/qualimap/bamqc/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
   tags:
     - qualimap
-    - qualimap_bamqc
+    - qualimap/bamqc
   files:
     - path: ./output/qualimap/test/qualimapReport.html
     - path: ./output/qualimap/test/genome_results.txt

tests/software/salmon/index/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
   tags:
     - salmon
-    - salmon_index
+    - salmon/index
   files:
     - path: ./output/index/salmon/ref_indexing.log
     - path: ./output/index/salmon/refseq.bin

tests/software/salmon/quant/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
   tags:
     - salmon
-    - salmon_quant
+    - salmon/quant
     - salmon_quant_single_end
   files:
     - path: ./output/salmon/test/cmd_info.json
@@ -54,7 +54,7 @@
   command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
   tags:
     - salmon
-    - salmon_quant
+    - salmon/quant
     - salmon_quant_paired_end
   files:
     - path: ./output/salmon/test/cmd_info.json

tests/software/samtools/faidx/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_faidx
+    - samtools/faidx
   files:
     - path: output/samtools/genome.fasta.fai
       md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5

tests/software/samtools/fastq/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/samtools/fastq -entry test_samtools_fastq -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_fastq
+    - samtools/fastq
   files:
     - path: output/samtools/test_2.fastq.gz
       md5sum: 229daf1a62d114cae42c65801e8c0114

tests/software/samtools/flagstat/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_flagstat
+    - samtools/flagstat
   files:
     - path: ./output/samtools/test_paired_end.sorted.bam.flagstat
       md5sum: 6d7934c303b15ce473f64d502b79984e

tests/software/samtools/idxstats/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_idxstats
+    - samtools/idxstats
   files:
     - path: ./output/samtools/test_paired_end.sorted.bam.idxstats
       md5sum: df60a8c8d6621100d05178c93fb053a2

tests/software/samtools/index/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_index
+    - samtools/index
   files:
     - path: output/samtools/test_paired_end.sorted.bam.bai
       md5sum: 704c10dd1326482448ca3073fdebc2f4

tests/software/samtools/merge/test.yml

@@ -2,6 +2,6 @@
   command: nextflow run ./tests/software/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_merge
+    - samtools/merge
   files:
     - path: output/samtools/test_merged.bam

tests/software/samtools/mpileup/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_mpileup
+    - samtools/mpileup
   files:
     - path: ./output/samtools/test.mpileup
       md5sum: 56c4cd5a4ecb7d6364878818f46ae256

tests/software/samtools/sort/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_sort
+    - samtools/sort
   files:
     - path: output/samtools/test.bam
       md5sum: 7e32f47768f922a73ccec4dc24db1973

tests/software/samtools/stats/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_stats
+    - samtools/stats
   files:
     - path: ./output/samtools/test_paired_end.sorted.bam.stats
       md5sum: 5f12c46ae4491b48611194c94093ebfb

tests/software/samtools/view/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
   tags:
     - samtools
-    - samtools_view
+    - samtools/view
   files:
     - path: output/samtools/test.bam
       md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13

tests/software/seacr/callpeak/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config
   tags:
     - seacr
-    - seacr_callpeak
+    - seacr/callpeak
   files:
     - path: output/seacr/test_1.stringent.bed
       md5sum: 3ac70475669eb6a7b8ca89e19a08a28e

tests/software/seqkit/split2/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
   tags:
     - seqkit
-    - seqkit_split2
+    - seqkit/split2
     - seqkit_split2_single_end
     - length
   files:
@@ -16,7 +16,7 @@
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
   tags:
     - seqkit
-    - seqkit_split2
+    - seqkit/split2
     - seqkit_split2_single_end
     - size
   files:
@@ -29,7 +29,7 @@
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
   tags:
     - seqkit
-    - seqkit_split2
+    - seqkit/split2
     - seqkit_split2_single_end
     - part
   files:
@@ -44,7 +44,7 @@
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
   tags:
     - seqkit
-    - seqkit_split2
+    - seqkit/split2
     - seqkit_split2_paired_end
     - length
   files:
@@ -61,7 +61,7 @@
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
   tags:
     - seqkit
-    - seqkit_split2
+    - seqkit/split2
     - seqkit_split2_paired_end
     - size
   files:
@@ -78,7 +78,7 @@
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
   tags:
     - seqkit
-    - seqkit_split2
+    - seqkit/split2
     - seqkit_split2_paired_end
     - part
   files:

tests/software/seqwish/induce/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/seqwish/induce -entry test_seqwish_induce -c tests/config/nextflow.config
   tags:
     - seqwish
-    - seqwish_induce
+    - seqwish/induce
   files:
     - path: output/seqwish/test.gfa
       md5sum: 216a02d3aca322a457c31a62c628548e

tests/software/shovill/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill_spades
+    - shovill/spades
   files:
     - path: output/shovill/contigs.gfa
       md5sum: 277af5d8ae8a0d2432db59a316226828
@@ -17,7 +17,7 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill_megahit -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill_megahit
+    - shovill/megahit
   files:
     - path: output/shovill/shovill.corrections
       md5sum: d41d8cd98f00b204e9800998ecf8427e
@@ -31,7 +31,7 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill_skesa -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill_skesa
+    - shovill/skesa
   files:
     - path: output/shovill/shovill.corrections
       md5sum: d41d8cd98f00b204e9800998ecf8427e
@@ -45,7 +45,7 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill_velvet -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill_velvet
+    - shovill/velvet
   files:
     # MD5sum not reproducible (timestamp, contig order)
     - path: output/shovill/contigs.fa

tests/software/star/align/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config
   tags:
     - star
-    - star_align
+    - star/align
     - star_align_single_end
   files:
     - path: output/star/star/Genome
@@ -40,7 +40,7 @@
   command: nextflow run ./tests/software/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - star
-    - star_align
+    - star/align
     - star_align_paired_end
   files:
     - path: output/star/star/Genome

tests/software/star/genomegenerate/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
   tags:
     - star
-    - star_genomegenerate
+    - star/genomegenerate
   files:
     - path: ./output/index/star/Genome
       md5sum: 323c992bac354f93073ce0fc43f222f8

tests/software/strelka/germline/test.yml

@@ -4,7 +4,7 @@
   command: nextflow run ./tests/software/strelka/germline -entry test_strelka_germline -c tests/config/nextflow.config
   tags:
     - strelka
-    - strelka_germline
+    - strelka/germline
   files:
     - path: output/strelka/strelka_test_variants.vcf.gz
     - path: output/strelka/strelka_test_variants.vcf.gz.tbi
@@ -14,7 +14,7 @@
   command: nextflow run ./tests/software/strelka/germline -entry test_strelka_germline_target_bed -c tests/config/nextflow.config
   tags:
     - strelka
-    - strelka_germline
+    - strelka/germline
   files:
     - path: output/strelka/strelka_test_variants.vcf.gz
     - path: output/strelka/strelka_test_variants.vcf.gz.tbi

tests/software/tabix/bgzip/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/tabix/bgzip -entry test_tabix_bgzip -c tests/config/nextflow.config
   tags:
     - tabix
-    - tabix_bgzip
+    - tabix/bgzip
   files:
     - path: ./output/tabix/test.vcf.gz
       md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d

tests/software/tabix/tabix/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_bed -c tests/config/nextflow.config
   tags:
     - tabix
-    - tabix_tabix
+    - tabix/tabix
     - bed
   files:
     - path: ./output/tabix/test.bed.gz.tbi
@@ -11,7 +11,7 @@
   command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
   tags:
     - tabix
-    - tabix_tabix
+    - tabix/tabix
     - gff
   files:
     - path: ./output/tabix/genome.gff3.gz.tbi
@@ -20,7 +20,7 @@
   command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
   tags:
     - tabix
-    - tabix_tabix
+    - tabix/tabix
     - vcf
   files:
     - path: output/tabix/test.vcf.gz.tbi

tests/software/tiddit/sv/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run ./tests/software/tiddit/sv -entry test_tiddit_sv -c tests/config/nextflow.config
   tags:
     - tiddit
-    - tiddit_sv
+    - tiddit/sv
     - vcf
   files:
     - path: output/tiddit/test.ploidy.tab
@@ -16,7 +16,7 @@
   command: nextflow run ./tests/software/tiddit/sv -entry test_tiddit_sv_no_ref -c tests/config/nextflow.config
   tags:
     - tiddit
-    - tiddit_sv
+    - tiddit/sv
     - vcf
   files:
     - path: output/tiddit/test.ploidy.tab

tests/software/ucsc/bed12tobigbed/test.yml

@@ -1,7 +1,7 @@
 - name: ucsc bed12tobigbed
   command: nextflow run ./tests/software/ucsc/bed12tobigbed -entry test_ucsc_bed12tobigbed -c tests/config/nextflow.config
   tags:
-    - ucsc_bed12tobigbed
+    - ucsc/bed12tobigbed
   files:
     - path: output/ucsc/test.bigBed
       md5sum: 98cf0d0baa3ae5a330c80afbb8bc2b18

tests/software/ucsc/bedgraphtobigwig/test.yml

@@ -1,7 +1,7 @@
 - name: ucsc bedgraphtobigwig
   command: nextflow run ./tests/software/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
   tags:
-    - ucsc_bedgraphtobigwig
+    - ucsc/bedgraphtobigwig
   files:
     - path: output/ucsc/test.bigWig
       md5sum: 5346de25b01ecbff91b63178b3bfbeec

tests/software/yara/index/test.yml

@@ -1,7 +1,7 @@
 - name: yara index test_yara_index
   command: nextflow run tests/software/yara/index -entry test_yara_index -c tests/config/nextflow.config
   tags:
-    - yara_index
+    - yara/index
     - yara
   files:
     - path: output/index/yara/yara.rid.limits

tests/software/yara/mapper/test.yml

@@ -2,7 +2,7 @@
   command: nextflow run tests/software/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config
   tags:
     - yara_single_end
-    - yara_mapper
+    - yara/mapper
     - yara
   files:
     - path: output/yara/test.mapped.bam
@@ -36,7 +36,7 @@
 - name: yara mapper test_yara_paired_end
   command: nextflow run tests/software/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config
   tags:
-    - yara_mapper
+    - yara/mapper
     - yara_paired_end
     - yara
   files: