From a3684d95947d642d6e31e731c938df3a9a2d8554 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 8 Apr 2021 03:10:52 -0500 Subject: [PATCH] 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 --- .github/workflows/pytest-workflow.yml | 20 +- tests/config/pytest_software.yml | 192 +++++++++--------- tests/software/bandage/image/test.yml | 2 +- tests/software/bcftools/consensus/test.yml | 2 +- tests/software/bcftools/filter/test.yml | 2 +- tests/software/bcftools/isec/test.yml | 2 +- tests/software/bcftools/merge/test.yml | 2 +- tests/software/bcftools/mpileup/test.yml | 2 +- tests/software/bcftools/stats/test.yml | 2 +- tests/software/bedtools/complement/test.yml | 2 +- tests/software/bedtools/genomecov/test.yml | 2 +- tests/software/bedtools/getfasta/test.yml | 2 +- tests/software/bedtools/intersect/test.yml | 2 +- tests/software/bedtools/maskfasta/test.yml | 2 +- tests/software/bedtools/merge/test.yml | 2 +- tests/software/bedtools/slop/test.yml | 2 +- tests/software/bedtools/sort/test.yml | 2 +- tests/software/bismark/align/test.yml | 4 +- tests/software/bismark/deduplicate/test.yml | 2 +- .../bismark/genomepreparation/test.yml | 2 +- .../bismark/methylationextractor/test.yml | 2 +- tests/software/bismark/report/test.yml | 2 +- tests/software/bismark/summary/test.yml | 2 +- tests/software/blast/blastn/test.yml | 2 +- tests/software/blast/makeblastdb/test.yml | 2 +- tests/software/bowtie/align/test.yml | 4 +- tests/software/bowtie/build_test/test.yml | 2 +- tests/software/bowtie2/align/test.yml | 4 +- tests/software/bowtie2/build_test/test.yml | 2 +- tests/software/bwa/index/test.yml | 2 +- tests/software/bwa/mem/test.yml | 4 +- tests/software/bwamem2/index/test.yml | 2 +- tests/software/bwamem2/mem/test.yml | 4 +- tests/software/bwameth/align/test.yml | 4 +- tests/software/bwameth/index/test.yml | 2 +- tests/software/cat/fastq/test.yml | 4 +- tests/software/dsh/filterbed/test.yml | 2 +- tests/software/dsh/splitbed/test.yml | 2 +- tests/software/gatk4/applybqsr/test.yml | 6 +- .../software/gatk4/baserecalibrator/test.yml | 8 +- .../software/gatk4/bedtointervallist/test.yml | 2 +- tests/software/gatk4/fastqtosam/test.yml | 4 +- .../software/gatk4/mergebamalignment/test.yml | 2 +- tests/software/gatk4/mergevcfs/test.yml | 6 +- tests/software/gatk4/revertsam/test.yml | 2 +- tests/software/gatk4/samtofastq/test.yml | 4 +- .../software/gatk4/splitncigarreads/test.yml | 2 +- .../software/gatk4/variantfiltration/test.yml | 2 +- tests/software/homer/annotatepeaks/test.yml | 2 +- tests/software/ivar/consensus/test.yml | 2 +- tests/software/ivar/trim/test.yml | 2 +- tests/software/ivar/variants/test.yml | 6 +- tests/software/kallisto/index/test.yml | 2 +- tests/software/kraken2/run/test.yml | 4 +- tests/software/methyldackel/extract/test.yml | 2 +- tests/software/methyldackel/mbias/test.yml | 2 +- tests/software/minimap2/align/test.yml | 4 +- .../picard/collectwgsmetrics/test.yml | 2 +- tests/software/picard/markduplicates/test.yml | 4 +- tests/software/picard/mergesamfiles/test.yml | 2 +- tests/software/preseq/lcextrap/test.yml | 4 +- tests/software/qualimap/bamqc/test.yml | 2 +- tests/software/salmon/index/test.yml | 2 +- tests/software/salmon/quant/test.yml | 4 +- tests/software/samtools/faidx/test.yml | 2 +- tests/software/samtools/fastq/test.yml | 2 +- tests/software/samtools/flagstat/test.yml | 2 +- tests/software/samtools/idxstats/test.yml | 2 +- tests/software/samtools/index/test.yml | 2 +- tests/software/samtools/merge/test.yml | 2 +- tests/software/samtools/mpileup/test.yml | 2 +- tests/software/samtools/sort/test.yml | 2 +- tests/software/samtools/stats/test.yml | 2 +- tests/software/samtools/view/test.yml | 2 +- tests/software/seacr/callpeak/test.yml | 2 +- tests/software/seqkit/split2/test.yml | 12 +- tests/software/seqwish/induce/test.yml | 2 +- tests/software/shovill/test.yml | 8 +- tests/software/star/align/test.yml | 4 +- tests/software/star/genomegenerate/test.yml | 2 +- tests/software/strelka/germline/test.yml | 4 +- tests/software/tabix/bgzip/test.yml | 2 +- tests/software/tabix/tabix/test.yml | 6 +- tests/software/tiddit/sv/test.yml | 4 +- tests/software/ucsc/bed12tobigbed/test.yml | 2 +- tests/software/ucsc/bedgraphtobigwig/test.yml | 2 +- tests/software/yara/index/test.yml | 2 +- tests/software/yara/mapper/test.yml | 4 +- 88 files changed, 233 insertions(+), 225 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index c7479963..e678aa54 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.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' diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index 4150faf4..cb865d0e 100644 --- a/tests/config/pytest_software.yml +++ b/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/** diff --git a/tests/software/bandage/image/test.yml b/tests/software/bandage/image/test.yml index 8c695af3..404edf62 100644 --- a/tests/software/bandage/image/test.yml +++ b/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 diff --git a/tests/software/bcftools/consensus/test.yml b/tests/software/bcftools/consensus/test.yml index 32c159ed..f36802a6 100644 --- a/tests/software/bcftools/consensus/test.yml +++ b/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 diff --git a/tests/software/bcftools/filter/test.yml b/tests/software/bcftools/filter/test.yml index 3b4d736a..f8bff320 100644 --- a/tests/software/bcftools/filter/test.yml +++ b/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 diff --git a/tests/software/bcftools/isec/test.yml b/tests/software/bcftools/isec/test.yml index 97520d8a..7aa1ffa0 100644 --- a/tests/software/bcftools/isec/test.yml +++ b/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 diff --git a/tests/software/bcftools/merge/test.yml b/tests/software/bcftools/merge/test.yml index 9686df01..88b826a7 100644 --- a/tests/software/bcftools/merge/test.yml +++ b/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 diff --git a/tests/software/bcftools/mpileup/test.yml b/tests/software/bcftools/mpileup/test.yml index 51711dd2..994acf64 100644 --- a/tests/software/bcftools/mpileup/test.yml +++ b/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 diff --git a/tests/software/bcftools/stats/test.yml b/tests/software/bcftools/stats/test.yml index 8a5d0c66..02c2e073 100644 --- a/tests/software/bcftools/stats/test.yml +++ b/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 diff --git a/tests/software/bedtools/complement/test.yml b/tests/software/bedtools/complement/test.yml index 433a0477..4fa55c13 100644 --- a/tests/software/bedtools/complement/test.yml +++ b/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 diff --git a/tests/software/bedtools/genomecov/test.yml b/tests/software/bedtools/genomecov/test.yml index 5460a8c8..a5faf5eb 100644 --- a/tests/software/bedtools/genomecov/test.yml +++ b/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 diff --git a/tests/software/bedtools/getfasta/test.yml b/tests/software/bedtools/getfasta/test.yml index a38a9cdf..1db28aa0 100644 --- a/tests/software/bedtools/getfasta/test.yml +++ b/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 diff --git a/tests/software/bedtools/intersect/test.yml b/tests/software/bedtools/intersect/test.yml index 717a1048..ddc91321 100644 --- a/tests/software/bedtools/intersect/test.yml +++ b/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 diff --git a/tests/software/bedtools/maskfasta/test.yml b/tests/software/bedtools/maskfasta/test.yml index 7ef998cc..24cd79b2 100644 --- a/tests/software/bedtools/maskfasta/test.yml +++ b/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 diff --git a/tests/software/bedtools/merge/test.yml b/tests/software/bedtools/merge/test.yml index 8f709ab0..83915d6e 100644 --- a/tests/software/bedtools/merge/test.yml +++ b/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 diff --git a/tests/software/bedtools/slop/test.yml b/tests/software/bedtools/slop/test.yml index adb8eb4a..5368c4e2 100644 --- a/tests/software/bedtools/slop/test.yml +++ b/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 diff --git a/tests/software/bedtools/sort/test.yml b/tests/software/bedtools/sort/test.yml index a4552158..7d45dca0 100644 --- a/tests/software/bedtools/sort/test.yml +++ b/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 diff --git a/tests/software/bismark/align/test.yml b/tests/software/bismark/align/test.yml index b79e5d0f..f51c66e0 100644 --- a/tests/software/bismark/align/test.yml +++ b/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 diff --git a/tests/software/bismark/deduplicate/test.yml b/tests/software/bismark/deduplicate/test.yml index ed6f7440..0de17541 100644 --- a/tests/software/bismark/deduplicate/test.yml +++ b/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 diff --git a/tests/software/bismark/genomepreparation/test.yml b/tests/software/bismark/genomepreparation/test.yml index 10e94f56..592b0887 100644 --- a/tests/software/bismark/genomepreparation/test.yml +++ b/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 diff --git a/tests/software/bismark/methylationextractor/test.yml b/tests/software/bismark/methylationextractor/test.yml index 8a0d218b..af88e733 100644 --- a/tests/software/bismark/methylationextractor/test.yml +++ b/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 diff --git a/tests/software/bismark/report/test.yml b/tests/software/bismark/report/test.yml index af4397d3..66a5d35d 100644 --- a/tests/software/bismark/report/test.yml +++ b/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 diff --git a/tests/software/bismark/summary/test.yml b/tests/software/bismark/summary/test.yml index 0489dbff..5816fc9d 100644 --- a/tests/software/bismark/summary/test.yml +++ b/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 diff --git a/tests/software/blast/blastn/test.yml b/tests/software/blast/blastn/test.yml index ac0cda0e..c45ee76d 100644 --- a/tests/software/blast/blastn/test.yml +++ b/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 diff --git a/tests/software/blast/makeblastdb/test.yml b/tests/software/blast/makeblastdb/test.yml index b393b1e6..81b06be0 100644 --- a/tests/software/blast/makeblastdb/test.yml +++ b/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 diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index 503eda09..18bd9151 100644 --- a/tests/software/bowtie/align/test.yml +++ b/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 diff --git a/tests/software/bowtie/build_test/test.yml b/tests/software/bowtie/build_test/test.yml index 67262eb8..cc5b3256 100644 --- a/tests/software/bowtie/build_test/test.yml +++ b/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 diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml index 1cb3d98b..27e54a66 100644 --- a/tests/software/bowtie2/align/test.yml +++ b/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 diff --git a/tests/software/bowtie2/build_test/test.yml b/tests/software/bowtie2/build_test/test.yml index 96385860..35e0f0c3 100644 --- a/tests/software/bowtie2/build_test/test.yml +++ b/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 diff --git a/tests/software/bwa/index/test.yml b/tests/software/bwa/index/test.yml index 413fa74e..553110e6 100644 --- a/tests/software/bwa/index/test.yml +++ b/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 diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml index aa1f9fbf..d5c23c16 100644 --- a/tests/software/bwa/mem/test.yml +++ b/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 diff --git a/tests/software/bwamem2/index/test.yml b/tests/software/bwamem2/index/test.yml index 7ec9435f..b4cc95f1 100644 --- a/tests/software/bwamem2/index/test.yml +++ b/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 diff --git a/tests/software/bwamem2/mem/test.yml b/tests/software/bwamem2/mem/test.yml index f5acaf83..c015e221 100644 --- a/tests/software/bwamem2/mem/test.yml +++ b/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 diff --git a/tests/software/bwameth/align/test.yml b/tests/software/bwameth/align/test.yml index ceb1bcf0..4b8779aa 100644 --- a/tests/software/bwameth/align/test.yml +++ b/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 diff --git a/tests/software/bwameth/index/test.yml b/tests/software/bwameth/index/test.yml index 79a53e50..d81de332 100644 --- a/tests/software/bwameth/index/test.yml +++ b/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 diff --git a/tests/software/cat/fastq/test.yml b/tests/software/cat/fastq/test.yml index cbaaafa7..d309e542 100644 --- a/tests/software/cat/fastq/test.yml +++ b/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 diff --git a/tests/software/dsh/filterbed/test.yml b/tests/software/dsh/filterbed/test.yml index 58b30b15..06285d05 100644 --- a/tests/software/dsh/filterbed/test.yml +++ b/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 diff --git a/tests/software/dsh/splitbed/test.yml b/tests/software/dsh/splitbed/test.yml index 63403813..c9cc80d7 100644 --- a/tests/software/dsh/splitbed/test.yml +++ b/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 diff --git a/tests/software/gatk4/applybqsr/test.yml b/tests/software/gatk4/applybqsr/test.yml index b17ffbe2..cbc9e3ed 100644 --- a/tests/software/gatk4/applybqsr/test.yml +++ b/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 diff --git a/tests/software/gatk4/baserecalibrator/test.yml b/tests/software/gatk4/baserecalibrator/test.yml index c0011152..a2ae8ebe 100644 --- a/tests/software/gatk4/baserecalibrator/test.yml +++ b/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 + - gatk4/baserecalibrator/intervals + - 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 diff --git a/tests/software/gatk4/bedtointervallist/test.yml b/tests/software/gatk4/bedtointervallist/test.yml index a8bb7bf0..7b4a5a62 100644 --- a/tests/software/gatk4/bedtointervallist/test.yml +++ b/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 diff --git a/tests/software/gatk4/fastqtosam/test.yml b/tests/software/gatk4/fastqtosam/test.yml index 2674ab59..6709d4c6 100644 --- a/tests/software/gatk4/fastqtosam/test.yml +++ b/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 diff --git a/tests/software/gatk4/mergebamalignment/test.yml b/tests/software/gatk4/mergebamalignment/test.yml index 2fb1be5f..852f57a5 100644 --- a/tests/software/gatk4/mergebamalignment/test.yml +++ b/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 diff --git a/tests/software/gatk4/mergevcfs/test.yml b/tests/software/gatk4/mergevcfs/test.yml index c461710b..833cd36b 100644 --- a/tests/software/gatk4/mergevcfs/test.yml +++ b/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 diff --git a/tests/software/gatk4/revertsam/test.yml b/tests/software/gatk4/revertsam/test.yml index 221975bf..d5a31664 100644 --- a/tests/software/gatk4/revertsam/test.yml +++ b/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 diff --git a/tests/software/gatk4/samtofastq/test.yml b/tests/software/gatk4/samtofastq/test.yml index a2a900a1..52267191 100644 --- a/tests/software/gatk4/samtofastq/test.yml +++ b/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 diff --git a/tests/software/gatk4/splitncigarreads/test.yml b/tests/software/gatk4/splitncigarreads/test.yml index 8f08899d..c20f28ef 100644 --- a/tests/software/gatk4/splitncigarreads/test.yml +++ b/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 diff --git a/tests/software/gatk4/variantfiltration/test.yml b/tests/software/gatk4/variantfiltration/test.yml index 9b9ac948..daa68b58 100644 --- a/tests/software/gatk4/variantfiltration/test.yml +++ b/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 diff --git a/tests/software/homer/annotatepeaks/test.yml b/tests/software/homer/annotatepeaks/test.yml index bbf964c9..f0ccd92f 100644 --- a/tests/software/homer/annotatepeaks/test.yml +++ b/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 diff --git a/tests/software/ivar/consensus/test.yml b/tests/software/ivar/consensus/test.yml index 02eaa20b..0c5db3f2 100644 --- a/tests/software/ivar/consensus/test.yml +++ b/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 diff --git a/tests/software/ivar/trim/test.yml b/tests/software/ivar/trim/test.yml index 6879ce6f..b0e94858 100644 --- a/tests/software/ivar/trim/test.yml +++ b/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 diff --git a/tests/software/ivar/variants/test.yml b/tests/software/ivar/variants/test.yml index 2eb665a7..642a501d 100644 --- a/tests/software/ivar/variants/test.yml +++ b/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 diff --git a/tests/software/kallisto/index/test.yml b/tests/software/kallisto/index/test.yml index afbe1d7d..77db7bbd 100644 --- a/tests/software/kallisto/index/test.yml +++ b/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 diff --git a/tests/software/kraken2/run/test.yml b/tests/software/kraken2/run/test.yml index 22fd4cdd..708ab51b 100644 --- a/tests/software/kraken2/run/test.yml +++ b/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 diff --git a/tests/software/methyldackel/extract/test.yml b/tests/software/methyldackel/extract/test.yml index 631aaf7a..19f10a55 100644 --- a/tests/software/methyldackel/extract/test.yml +++ b/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 diff --git a/tests/software/methyldackel/mbias/test.yml b/tests/software/methyldackel/mbias/test.yml index 9d63f2fe..73cc4fbe 100644 --- a/tests/software/methyldackel/mbias/test.yml +++ b/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 diff --git a/tests/software/minimap2/align/test.yml b/tests/software/minimap2/align/test.yml index 9fdf1753..b8ddde21 100644 --- a/tests/software/minimap2/align/test.yml +++ b/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 diff --git a/tests/software/picard/collectwgsmetrics/test.yml b/tests/software/picard/collectwgsmetrics/test.yml index 2e9f0f22..ef76fb4c 100644 --- a/tests/software/picard/collectwgsmetrics/test.yml +++ b/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 diff --git a/tests/software/picard/markduplicates/test.yml b/tests/software/picard/markduplicates/test.yml index 021c7a22..0de69083 100644 --- a/tests/software/picard/markduplicates/test.yml +++ b/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 diff --git a/tests/software/picard/mergesamfiles/test.yml b/tests/software/picard/mergesamfiles/test.yml index 46a790fa..4f060fbe 100644 --- a/tests/software/picard/mergesamfiles/test.yml +++ b/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 diff --git a/tests/software/preseq/lcextrap/test.yml b/tests/software/preseq/lcextrap/test.yml index 7e1552f7..e511dd40 100644 --- a/tests/software/preseq/lcextrap/test.yml +++ b/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 diff --git a/tests/software/qualimap/bamqc/test.yml b/tests/software/qualimap/bamqc/test.yml index edc010dd..404b5cf8 100644 --- a/tests/software/qualimap/bamqc/test.yml +++ b/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 diff --git a/tests/software/salmon/index/test.yml b/tests/software/salmon/index/test.yml index efd3dac1..fee68bd0 100644 --- a/tests/software/salmon/index/test.yml +++ b/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 diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml index 4bd64059..12fb94a1 100644 --- a/tests/software/salmon/quant/test.yml +++ b/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 diff --git a/tests/software/samtools/faidx/test.yml b/tests/software/samtools/faidx/test.yml index 912ea8d9..37d59d2c 100644 --- a/tests/software/samtools/faidx/test.yml +++ b/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 diff --git a/tests/software/samtools/fastq/test.yml b/tests/software/samtools/fastq/test.yml index ac89b510..f9c736a2 100644 --- a/tests/software/samtools/fastq/test.yml +++ b/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 diff --git a/tests/software/samtools/flagstat/test.yml b/tests/software/samtools/flagstat/test.yml index 7f397083..7cfba127 100644 --- a/tests/software/samtools/flagstat/test.yml +++ b/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 diff --git a/tests/software/samtools/idxstats/test.yml b/tests/software/samtools/idxstats/test.yml index 34220292..8f4c8028 100644 --- a/tests/software/samtools/idxstats/test.yml +++ b/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 diff --git a/tests/software/samtools/index/test.yml b/tests/software/samtools/index/test.yml index 87934bfb..79b541b4 100644 --- a/tests/software/samtools/index/test.yml +++ b/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 diff --git a/tests/software/samtools/merge/test.yml b/tests/software/samtools/merge/test.yml index 27ec9f31..c9d2c1f6 100644 --- a/tests/software/samtools/merge/test.yml +++ b/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 diff --git a/tests/software/samtools/mpileup/test.yml b/tests/software/samtools/mpileup/test.yml index 5830b455..8088e2ef 100644 --- a/tests/software/samtools/mpileup/test.yml +++ b/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 diff --git a/tests/software/samtools/sort/test.yml b/tests/software/samtools/sort/test.yml index f9ed2227..fc7ff858 100644 --- a/tests/software/samtools/sort/test.yml +++ b/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 diff --git a/tests/software/samtools/stats/test.yml b/tests/software/samtools/stats/test.yml index 86223dae..714cb550 100644 --- a/tests/software/samtools/stats/test.yml +++ b/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 diff --git a/tests/software/samtools/view/test.yml b/tests/software/samtools/view/test.yml index 308fde3f..95867c5a 100644 --- a/tests/software/samtools/view/test.yml +++ b/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 diff --git a/tests/software/seacr/callpeak/test.yml b/tests/software/seacr/callpeak/test.yml index e8e4bef0..d110df9a 100644 --- a/tests/software/seacr/callpeak/test.yml +++ b/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 \ No newline at end of file diff --git a/tests/software/seqkit/split2/test.yml b/tests/software/seqkit/split2/test.yml index 269f0ea1..ccdd01d2 100644 --- a/tests/software/seqkit/split2/test.yml +++ b/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: diff --git a/tests/software/seqwish/induce/test.yml b/tests/software/seqwish/induce/test.yml index 4fb7cba7..ed657a84 100644 --- a/tests/software/seqwish/induce/test.yml +++ b/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 diff --git a/tests/software/shovill/test.yml b/tests/software/shovill/test.yml index a3072b3a..9894b1d0 100644 --- a/tests/software/shovill/test.yml +++ b/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 diff --git a/tests/software/star/align/test.yml b/tests/software/star/align/test.yml index 8e0733a6..e4bbdb51 100644 --- a/tests/software/star/align/test.yml +++ b/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 diff --git a/tests/software/star/genomegenerate/test.yml b/tests/software/star/genomegenerate/test.yml index ac7464e2..02b98ee3 100644 --- a/tests/software/star/genomegenerate/test.yml +++ b/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 diff --git a/tests/software/strelka/germline/test.yml b/tests/software/strelka/germline/test.yml index 1db335a9..43b95e54 100644 --- a/tests/software/strelka/germline/test.yml +++ b/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 diff --git a/tests/software/tabix/bgzip/test.yml b/tests/software/tabix/bgzip/test.yml index 7e284124..c3775d47 100644 --- a/tests/software/tabix/bgzip/test.yml +++ b/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 diff --git a/tests/software/tabix/tabix/test.yml b/tests/software/tabix/tabix/test.yml index 65820a34..73724fb8 100644 --- a/tests/software/tabix/tabix/test.yml +++ b/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 diff --git a/tests/software/tiddit/sv/test.yml b/tests/software/tiddit/sv/test.yml index 50b2f0f2..4cc0f910 100644 --- a/tests/software/tiddit/sv/test.yml +++ b/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 diff --git a/tests/software/ucsc/bed12tobigbed/test.yml b/tests/software/ucsc/bed12tobigbed/test.yml index 58641edf..9aadf265 100644 --- a/tests/software/ucsc/bed12tobigbed/test.yml +++ b/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 diff --git a/tests/software/ucsc/bedgraphtobigwig/test.yml b/tests/software/ucsc/bedgraphtobigwig/test.yml index 43ebc22c..c2476623 100644 --- a/tests/software/ucsc/bedgraphtobigwig/test.yml +++ b/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 diff --git a/tests/software/yara/index/test.yml b/tests/software/yara/index/test.yml index 8942b27d..3ab1fb1f 100644 --- a/tests/software/yara/index/test.yml +++ b/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 diff --git a/tests/software/yara/mapper/test.yml b/tests/software/yara/mapper/test.yml index cb364d85..311824e6 100644 --- a/tests/software/yara/mapper/test.yml +++ b/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: